Use of IMP3 as a Prognostic Marker for Cancer

ABSTRACT

Provided herein are methods and compositions for the prognostic evaluation of a patient suspected of having, or having, cancer by assessing the expression of IMP3 in a biological sample of a patient. Methods can be used at the time of initial diagnosis of malignant tumors to identify a group of patients with a high potential to develop progression or metastasis later. Therefore, methods not only are able to provide very useful prognostic information for patients but also can help clinicians to select a candidate patient likely to benefit from early and aggressive cancer therapy. Methods and compositions for the treatment of cancer associated with expression of IMP3 are also provided.

RELATED APPLICATIONS

This application is a continuation-in-part of U.S. Ser. No. 11/758,382,which was filed on Jun. 5, 2007 and claims the benefit of priority toU.S. provisional applications 60/811,702 filed Jun. 6, 2006 and60/813,216, filed Jun. 12, 2006, all of which are specificallyincorporated herein by reference in their entirety.

BACKGROUND

In spite of numerous advances in medical research, cancer remains aleading cause of death in the United States. Traditional modes ofclinical care, such as surgical resection, radiotherapy andchemotherapy, have a significant failure rate, especially for solidtumors. Failure occurs either because the initial tumor is unresponsive,or because of recurrence due to regrowth at the original site and/ormetastases. The etiology, diagnosis and ablation of cancer remain acentral focus for medical research and development.

While different forms of cancer have different properties, one factorwhich many cancers share is the ability to metastasize. Distantmetastasis of all malignant tumors remains the primary cause of death inpatients with the disease. Patients with metastatic disease aretypically treated with systemic therapy, which is associated withsubstantial toxicity. Unless the patient presents with metastaticdisease, clinical observation is typically used to prognose the diseasefollowing surgical resection. Currently, the methods to determineprognosis and select patients for adjuvant therapy rely mainly onpathological and clinical staging. However, it is very difficult topredict which localized tumor will eventuate in distant metastasis.

Since the chance for complete remission of cancer is, in most cases,greatly enhanced by accurate prognosis, it is desirable that physiciansbe able to determine the metastatic potential of tumors. However, themetastatic potential of localized cancers is often unpredictable. Thedevelopment of methods that permit rapid and accurate detection of manyforms of cancers continues to challenge the medical community. Thus amajor problem in the treatment of cancer remains detection andprognosis, which enables appropriate therapeutic treatment resulting insuccessful treatment in many cases. Therefore, there is a great need forthe identification of biomarkers that can accurately distinguishlocalized tumors with a high probability of metastasis from those thatwill remain indolent. Using such biomarkers, one can predict thepatient's prognosis and can effectively target the individuals who wouldmost likely benefit from adjuvant therapy.

SUMMARY

The present invention is based at least in part on the finding that theexpression of IMP3 is strongly associated with tumor metastasis and poorprognosis. IMP3 thus serves as an independent prognostic biomarker topredict cancer metastasis and a potential target protein to treatmetastatic cancer.

Provided herein are methods for predicting the prognosis of a subjecthaving a cancerous tumor. The method may comprise determining the levelof IMP3 in a cancerous tumor of a subject, wherein a higher level ofIMP3 in the cancerous tissue of the subject, e.g., relative to that in acontrol indicates that the prognosis of the subject is poor, whereas anundetectable or a lower or similar level of IMP3 in the cancerous tissueof the subject relative to that in the control indicates that theprognosis of the subject is good. A method may also comprise determiningthe presence of IMP3 in a cancerous tissue in a subject, wherein thepresence of IMP3 in the cancerous tissue indicates that the prognosis ofthe subject is poor. Determining the level of IMP3 may comprisedetermining the level of IMP3 protein, e.g., by immunohistochemicalstaining, which may be followed by computerized image analysis forquantitative immunohistochemistry. A control may be the level of IMP3 innon-cancerous cells of the same origin as those of the cancerous tumoror the level of IMP3 in cells of a cancerous tumor that has a goodprognosis. The cancerous tumor may be a renal tumor or a urinary bladdertumor. The method further comprises first obtaining a biopsy of acancerous tumor of the subject.

A prognostic method may also comprise determining the presence or levelof IMP3 and evaluate another prognostic factor, e.g., the stage of thetumor.

Also provided herein are methods for treating a subject having acancerous tumor. A method may comprise (i) determining the level of IMP3in the cancerous tumor of a subject; and (ii) if the level of IMP3 inthe cancerous tumor of a subject is more similar to that of a canceroustumor of a subject having a poor prognosis rather than that of a subjecthaving a good prognosis, treating the subject aggressively, whereas ifthe level of IMP3 in the cancerous tumor of a subject is more similar tothat of a cancerous tumor of a subject having a good prognosis ratherthan that of a subject having a poor prognosis, treating the subjectless aggressively. Instead of determining a level of IMP3 and comparingit to a control, a method may comprise determining the presence of IMP3,wherein the presence of IMP3 indicates that the subject should betreated aggressively.

Further provided herein are kits, e.g., kits comprising one or moreagents for detecting the level of IMP3. A kit may also comprise acontrol. The agent for detecting the level of IMP3 may be an antibody ora variant, e.g., a fragment, thereof. A control may be the level of IMP3in a cancerous tumor having a good prognosis or it may be a sample of ahealthy subject. A kit may also comprise one or more other biomarkers orreagents for evaluating other prognostic factors.

Other methods provided herein are methods for monitoring the progressionof a cancer in a subject. A method may comprise monitoring the level ofIMP3 in a cancerous tumor of the subject over time, wherein an increasein the level of IMP3 in a cancerous tumor of the subject indicates thatthe cancer is progressing.

Therapeutic methods are also provided herein. An exemplary method fortreating a subject having a cancer associated with high levels of IMP3,comprises administering to the subject a therapeutically effectiveamount of an agent that reduces the level or activity of IMP3, such asby directly targeting IMP3 protein or its expression or by targeting anIMP3 target, such as insulin-like growth factor II (IGF-II).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Expression of IMP3 in primary and metastatic renal cellcarcinomas. Immunohistochemical stains for IMP3 showing that metastaticRCC in the bone (A) and primary RCC with subsequent development ofmetastasis (B) were positive for IMP3 while primary RCC withoutmetastasis (C) were negative for IMP3.

FIG. 2. The percentage of IMP3 expression in patients with primary RCCswithout metastasis (Met), primary RCCs with metastasis (Met) andmetastatic (Met) RCCs.

FIG. 3. Western blot analysis of IMP3 expression in primary RCCs.Metastatic RCC cell line (Cell Line) was used for comparison. Actin wasincluded as a loading control. Primary RCCs with Met=primary RCCs withmetastasis; RCCs without Met=primary RCCs without metastasis. (Lower)Bar graph showing IMP3 protein levels in above Western blot analysis(case 1-3=RCCs with Met; case 4-5=primary RCCs without Met) and IMP3mRNA Levels by quantitative real-time PCR analysis in the same sample. Aratio of IMP3 protein expression in Western blot analysis was calculatedrelative to actin expression and a ratio of IMP3 mRNA expression inquantitative real-time PCR analysis was calculated relative to thehousekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH)expression. IHC=immunohistochemistry; “+”=positive for IMP3 staining byIHC; “−”=negative for IMP3 staining by IHC.

FIG. 4. Kaplan-Meier analysis of metastasis-free (A) and overallsurvivals (B) according to IMP3 status (positive verses negative)assessed by immunohistochemical analysis in total 371 patients withlocalized primary RCCs without metastasis during surgery. P values werecalculated by using the log-rank test.

FIG. 5. Kaplan-Meier analysis of metastasis-free and overall survivalsin stage I patients (n=216, A and B), stage II patients (n=64, C and D)and stage III patients (n=91, E and F) according to IMP3 status(positive verses negative) with localized primary RCCs assessed byimmunohistochemical analysis. P values were calculated by using thelog-rank test.

FIG. 6: Association of IMP3 tumor expression with progression to distantmetastases for 317 patients with localized papillary and chromophobeRCC. Metastases-free survival rates (SE, number still at risk) at 5 and10 years following nephrectomy were 63.9% (8.8%, 17) and 48.6% (9.5%,12), respectively, for patients with IMP3-positive tumors compared with97.7% (0.9%, 223) and 93.5% (1.9%, 86), respectively, for patients withIMP3-negative tumors.

FIG. 7: Association of IMP3 tumor expression with death for 317 patientswith localized papillary and chromophobe RCC. Overall survival rates(SE, number still at risk) at 5 and 10 years following nephrectomy were57.9% (9.0%, 17) and 47.1% (9.2%, 12), respectively, for patients withIMP3-positive tumors compared with 85.0% (2.2%, 223) and 67.4% (3.3%,86), respectively, for patients with IMP3-negative tumors.

FIG. 8 shows the probability of metastasis free survival as a functionof metastasis-free survival time (years) for stage 1, 2 and 3 RCCs.

FIG. 9 shows the shows the probability of metastasis free survival as afunction of metastasis-free survival time (years after surgery) forstages 1, 2 and 3 RCCs and negative, low positive or high positive IMP3expression.

FIG. 10. Immunohistochemical stains for IMP3 showing that high grade UC(A) was positive for IMP3 while low grade UC (B) was negative for IMP3.

FIG. 11. Kaplan-Meier analysis of progression-free (A) and disease-freesurvival (B) in patients with superficial urothelial carcinomas (Ta, T1and Tis). P values were calculated by using the log-rank test.

FIG. 12. Kaplan-Meier analysis of progression-free survivals in patientswith Ta superficial urothelial carcinomas (A) and T1 superficialurothelial carcinomas (B). P values were calculated by using thelog-rank test.

FIG. 13. Kaplan-Meier analysis of metastasis-free survivals in patientswith T1 superficial urothelial carcinomas. P values were calculated byusing the log-rank test.

DETAILED DESCRIPTION Definitions

“Cancers of epithelial origin” refers to “carcinomas” that arise fromepithelial cells which include, but are not limited to, skin cancer,such as squamous cell and basal cell cancers, lung cancer, breastcancer, prostate cancer, renal cell carcinoma, liver cancer, urinarybladder cancer, ovarian cancer, cervical cancer, endometrial cancer,gastrointestinal cancers including esophageal cancer, small bowelcancer, stomach cancer, colon cancer and other known cancers that effectepithelial cells throughout the body.

The term “aggressive” or “invasive” with respect to cancer refers to theproclivity of a tumor for expanding beyond its boundaries into adjacenttissue (Darnell, J. (1990), Molecular Cell Biology, Third Ed., W. H.Freeman, N.Y.). Invasive cancer can be contrasted with organ-confinedcancer wherein the tumor is only in a particular organ. The invasiveproperty of a tumor is often accompanied by the elaboration ofproteolytic enzymes, such as collagenases, that degrade matrix materialand basement membrane material to enable the tumor to expand beyond theconfines of the capsule, and beyond confines of the particular tissue inwhich that tumor is located.

The term “metastasis”, as used herein, refers to the condition of spreadof cancer from the organ of origin to additional distal sites in thepatient. The process of tumor metastasis is a multistage event involvinglocal invasion and destruction of intercellular matrix, intravasationinto blood vessels, lymphatics or other channels of transport, survivalin the circulation, extravasation out of the vessels in the secondarysite and growth in the new location (Fidler, et al., Adv. Cancer Res.28, 149-250 (1978), Liotta, et al., Cancer Treatment Res. 40, 223-238(1988), Nicolson, Biochim. Biophy. Acta 948, 175-224 (1988) and Zetter,N. Eng. J. Med. 322, 605-612 (1990)). Increased malignant cell motilityhas been associated with enhanced metastatic potential in animal as wellas human tumors (Hosaka, et al., Gann 69, 273-276 (1978) and Haemmerlin,et al., Int. J. Cancer 27, 603-610 (1981)).

A “biological sample” refers to a sample of biological material obtainedfrom a subject, preferably a human subject, including a tissue, a tissuesample, a cell sample, a tumor sample, and a biological fluid, e.g.,blood, urine, and a nipple aspirate. A biological sample may be obtainedin the form of, e.g., a tissue biopsy, such as, an aspiration biopsy, abrush biopsy, a surface biopsy, a needle biopsy, a punch biopsy, anexcision biopsy, an open biopsy, an incision biopsy and an endoscopicbiopsy.

An “isolate” of a biological sample (e.g., an isolate of a tissue ortumor sample) refers to a material or composition (e.g., a biologicalmaterial or composition) which has been separated, derived, extracted,purified or isolated from the sample and preferably is substantiallyfree of undesirable compositions and/or impurities or contaminantsassociated with the biological sample.

A “tissue sample” includes a portion, piece, part, segment, or fractionof a tissue which is obtained or removed from an intact tissue of asubject, preferably a human subject.

A “tumor sample” includes to a portion, piece, part, segment, orfraction of a tumor, for example, a tumor which is obtained or removedfrom a subject (e.g., removed or extracted from a tissue of a subject),preferably a human subject.

A “tumor” refers to an abnormal growth of cells.

A “primary tumor” is a tumor appearing at a first site within thesubject and can be distinguished from a “metastatic tumor” which appearsin the body of the subject at a remote site from the primary tumor.

A “patient” refers to any warm-blooded animal, preferably a human.

Prognostic and Diagnostic Biomarker and Methods

The present invention provides methods for predicting or determining theprognosis, e.g., likelihood of metastasis or aggressive behavior, insubjects with malignant tumors. A method may comprise measuring thelevel of expression of IMP3 present in a biological sample obtained froma patient and comparing the observed level with one or a range of IMP3levels normally found in biological samples (of the same type) ofhealthy individuals. A high level of IMP3 expression is indicative of agreater potential for metastatic activity or aggressive behavior andcorresponds to a poor prognosis, while very low or undetectable levelsindicate that the tumor is less aggressive and correspond to a betterprognosis.

An exemplary method, e.g., for predicting the prognosis of a subjecthaving a cancerous tumor, comprises determining the presence of IMP3 ina cancerous tumor of a subject, wherein the presence of IMP3 in thecancerous tissue of the subject indicates that the prognosis of thesubject is poor, whereas the absence of IMP3 in the cancerous tissue ofthe subject indicates that the prognosis of the subject is good. Amethod may also comprise determining the level of expression of IMP3 ina cancerous tumor of a subject, wherein a higher level of expression ofIMP3 in the cancerous tissue of the subject relative to a control value,e.g., level in a control, indicates that the prognosis of the subject ispoor, whereas a lower or similar level of expression of IMP3 in thecancerous tissue of the subject relative to that in the controlindicates that the prognosis of the subject is good. A poor prognosisindicates that the cancer is of an aggressive or invasive type, likelyto progress fast and/or likely to metastasize.

IMP3 is an oncofetal protein and is a member of the insulin-like growthfactor II (IGF-II) mRNA binding protein (IMP) family that consists ofIMP1, IMP2 and IMP3¹¹. IMP family members play an important role in RNAtrafficking and stabilization, cell growth, and cell migration duringthe early stages of embryogenesis¹². The IMP3 gene is located onchromosome 7p11.2±11cM¹³ and is identical to the KOC (KH domaincontaining protein overexpressed in cancer) protein that was originallycloned from a pancreatic tumor cDNA screen¹⁴. IMP3 is expressed indeveloping epithelium, muscle and placenta during early stages of humanand mouse embryogenesis, but it is expressed at low or undetectablelevels in adult tissues^(11,12). The amino acid sequence of the humanIMP3 protein is set forth in GenBank Accession Nos. AAC35208 andNP_(—)006538.2 and is encoded by the nucleotide sequence set forth inGenBank Accession Nos. U97188 and NM_(—)006547.2. The protein hasseveral RNA recognition motifs and K homology RNA-binding domains, typeI (see GenBank entries). The nucleotide and amino acid sequences of thehuman IMP3 protein are set forth below:

(SEQ ID NO: 1) atgaacaaactgtatatcggaaacctcagcgagaacgccgccccctcggacctagaaagtatcttcaaggacgccaagatcccggtgtcgggacccttcctggtgaagactggctacgcgttcgtggactgcccggacgagagctgggccctcaaggccatcgaggcgctttcaggtaaaatagaactgcacgggaaacccatagaagttgagcactcggtcccaaaaaggcaaaggattcggaaacttcagatacgaaatatcccgcctcatttacagtgggaggtgctggatagtttactagtccagtatggagtggtggagagctgtgagcaagtgaacactgactcggaaactgcagttgtaaatgtaacctattccagtaaggaccaagctagacaagcactagacaaactgaatggatttcagttagagaatttcaccttgaaagtagcctatatccctgatgaaatggccgcccagcaaaaccccttgcagcagccccgaggtcgccgggggcttgggcagaggggctcctcaaggcaggggtctccaggatccgtatccaagcagaaaccatgtgatttgcctctgcgcctgctggttcccacccaatttgttggagccatcataggaaaagaaggtgccaccattcggaacatcaccaaacagacccagtctaaaatcgatgtccaccgtaaagaaaatgcgggggctgctgagaagtcgattactatcctctctactcctgaaggcacctctgcggcttgtaagtctattctggagattatgcataaggaagctcaagatataaaattcacagaagagatccccttgaagattttagctcataataactttgttggacgtcttattggtaaagaaggaagaaatcttaaaaaaattgagcaagacacagacactaaaatcacgatatctccattgcaggaattgacgctgtataatccagaacgcactattacagttaaaggcaatgttgagacatgtgccaaagctgaggaggagatcatgaagaaaatcagggagtcttatgaaaatgatattgcttctatgaatcttcaagcacatttaattcctggattaaatctgaacgccttgggtctgttcccacccacttcagggatgccacctcccacctcagggcccccttcagccatgactcctccctacccgcagtttgagcaatcagaaacggagactgttcatctgtttatcccagctctatcagtcggtgccatcatcggcaagcagggccagcacatcaagcagctttctcgctttgctggagcttcaattaagattgctccagcggaagcaccagatgctaaagtgaggatggtgattatcactggaccaccagaggctcagttcaaggctcagggaagaatttatggaaaaattaaagaagaaaactttgttagtcctaaagaagaggtgaaacttgaagctcatatcagagtgccatcctttgctgctggcagagttattggaaaaggaggcaaaacggtgaatgaacttcagaatttgtcaagtgcagaagttgttgtccctcgtgaccagacacctgatgagaatgaccaagtggttgtcaaaataactggtcacttctatgcttgccaggttgcccagagaaaaattcaggaaattctgactcaggtaaagcagcaccaacaacagaaggctctgcaaagtggaccacctcagtcaagacggaagtaa (SEQ ID NO: 2)MNKLYIGNLSENAAPSDLESIFKDAKIPVSGPFLVKTGYAFVDCPDESWALKAIEALSGKIELHGKPIEVEHSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQQNPLQQPRGRRGLGQRGSSRQGSPGSVSKQKPCDLPLRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILSTPEGTSAACKSILEIMHKEAQDIKFTEEIPLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQELTLYNPERTITVKGNVETCAKAEEEIMKKIRESYENDIASMNLQAHLIPGLNLNALGLFPPTSGMPPPTSGPPSAMTPPYPQFEQSETETVHLFIPALSVGAIIGKQGQHIKQLSRFAGASIKIAPAEAPDAKVRMVIITGPPEAQFKAQGRIYGKIKEENFVSPKEEVKLEAHIRVPSFAAGRVIGKGGKTVNELQNLSSAEVVVPRDQTPDENDQVVVKITGHFYACQVAQRKIQEILTQVKQHQQQKALQSGPPQSRRK

Determining the presence or the level of IMP3 (or expression of IMP3) ina cell or a biological sample includes determining qualitatively orquantitatively the presence of IMP3 protein or degradation productthereof, the presence of IMP3 mRNA or pre-mRNA, or the presence of anybiological molecule or product that is indicative of IMP3 expression, ordegradation product thereof. The level of IMP3 may also be determined bydetecting and/or measuring the level of IMP3 autoantibodies.

It may be sufficient to detect the presence of IMP3 rather thandetermining its level and comparing it to a standard or control level,as IMP3 levels are relatively low in normal cells and tissues and maynot be detectable by the usual methods of detection, e.g.,immunohistochemistry. However, when comparing an IMP3 level to a controllevel, a control may be a value that corresponds to the level of IMP3 ina normal or healthy tissue of the same type as that from which a samplewas obtained. A control may also be an average or mean value of at least2, 5, 10 or more values of levels of IMP3 in normal or healthy tissues.A control may also be a normal control sample, i.e., a sample obtainedfrom a normal or healthy individual, or an individual that does not havecancer, or at least not the type of cancer that is being investigated. Acontrol may also be a value obtained from non-cancerous tissue that isadjacent to the cancerous tissue from which a value was obtained.

In one embodiment, a value obtained from a subject is compared to othervalues, e.g., control values, present in computer readable form. Forexample, a value obtained from a subject may be entered into analgorithm or software program comprising one or more values, e.g.,control values, and values from cancerous specimens, and a comparison iseffected by the software program. A software program may also provide aconclusion based on the comparison, e.g., likelihood of cancerprogression or metastasis.

For purposes of comparison, a test sample and normal control sample maybe of the same type, that is, obtained from the same biological source.A normal control sample can also be a standard sample that contains thesame concentration of IMP3 that is normally found in a biological sampleof the same type and that is obtained from a healthy individual, e.g.,an individual who does not have cancer. For example, there can be astandard normal control sample for the amounts of IMP3 normally found ina cell or tissue.

When comparing an IMP3 level to a control value, a poor prognosis may beconcluded from the presence of at least about 50%, 2 fold, 5 fold, 10fold, 30 fold, 50 fold, 100 fold or more IMP3 in the sample of thesubject compared to the control value. The term “higher level” in thecontext of levels of IMP3 in a sample from a patient relative to acontrol value of the level in a tissue from a healthy subject refers toa level that is statistically significant or significantly above levelsfound in the control value or tissue from the healthy subject. The term“statistically significant” or “significantly” refers to statisticalsignificance and generally means a two standard deviation (2SD) abovenormal, or higher, concentration of the marker. The levels of IMP3 canbe represented by arbritary units, for example as units obtained from adensitometer, luminometer, or an ELISA plate reader. Ratios ordifferences in number of units from a cancerous sample and number ofunits from a control sample, e.g., an adjacent non-cancerous tissue, maybe used to determine the prognosis of the patient from whom the sampleswere taken. These ratios and differences are further discussed herein inthe context of particular methods of detection of IMP3 mRNA or protein.

Generally, the presence or amount of IMP3 will be determined in a sampleobtained from a tumor. However, it may also be possible that high IMP3levels located on cells other than the tumor cells (e.g., red or whiteblood cells) is indicative of a bad prognosis of a cancer, in which caseone could determine IMP3 presence or levels in these other cells. Acontrol value or sample would then be obtained from the same type ofcells.

A sample may be obtained from a primary tumor. Alternatively, it mayalso be obtained from a metastatic tumor. A sample may be obtained froma surgically removed tumor, e.g., from a kidney tumor. In oneembodiment, a sample is obtained from tissue removed in a radical orpartial nephrectomy. When a nephrectomy is performed, IMP3 levels may bemeasured in cancerous tissue as well as in non-cancerous tissue of thekidney. Similarly, when a tissue or organ is removed for treatinganother type of cancer, a cancerous sample and a control sample may beobtained from the same tissue or organ.

The level of IMP3 may be determined directly in a biological specimen,e.g., a biopsy, obtained from a subject. Depending on the method used todetermine the level of IMP3, it may be desirable to treat a biologicalspecimen prior to measuring the level of IMP3. For example, one or morecells may be isolated from the biological specimen. Fractions of thespecimen may be prepared. In other cases, proteins or specific proteinsmay be isolated or purified from of the sample. In other cases, nucleicacids, e.g., RNA may be isolated or purified from of the sample. Forexample, in a case when IMP3 protein is detected or measured, one maywish to isolate proteins from the sample, and one may even want toisolate IMP3 proteins from most of the other proteins. When IMP3 mRNA isdetected or measured, one may want to isolate total RNA from the sample,and optionally isolate and/or amplify IMP3 mRNA.

The methods described herein are useful for predicting the prognosis ofsubjects having any one of a variety of cancers. For example, the cancercan be kidney cancer, e.g., renal cell carcinoma (RCC). RCC embraces agroup of renal cancers, all of which are derived from the renal tubularepithelium but each with distinct clinical, pathologic, and genotypicfeatures. Examples of RCC include clear cell RCC, papillary RCC,chromophobe RCC, and collecting duct carcinoma. The RCC may be a stageI, II, III or IV. Stages I-III (T3, N0, M0) tumors define localized RCC,whereas most of stage IV tumors defines metastasized RCC.

Other cancers include urogenital cancer, e.g., urothelial carcinomas inurinary bladder, kidney, pelvic and ureter. An example bladder carcinomais urothelial carcinoma of the bladder. The majority (75%) of thesecarcinomas are early stages (i.e., stage Ta and T1) of superficialurothelial carcinomas and can be prognosed and diagnosed as describedherein. Generally, the following other tumors or carcinomas of thebladder can also be prognosed and diagnosed as described herein:urothelial (transitional cell) carcinoma, including noninvasiveurothelial tumors, invasive urothelial tumors, superficial urothelialtumors, papillary urothelial tumors (invasive or non invasive),papillomas, papillary urothelial neoplasms of low malignant potential,papillary urothelial carcinoma (low grade or high grade), flaturothelial tumors, noninvasive flat urothelial carcinomas, flatcarcinoma in situ (cis), and flat invasive urothelial carcinomas.

Other cancers whose development may potentially be prognosticated asdescribed herein include melanoma, prostate carcinoma, lung carcinomas(non-small cell carcinoma, small cell carcinoma, neuroendocrinecarcinoma and carcinoid tumor), breast carcinomas (ductal carcinoma,lobular carcinoma and mixed ductal and lobular carcinoma), thyroidcarcinomas (papillary thyroid carcinoma, follicular carcinoma andmedullary carcinoma), brain cancers (meningioma, astrocytoma,glioblastoma, cerebellum tumors, medulloblastoma, ependymoma),pancreatic carcinoma, ovarian carcinomas (serous, mucinous andendometrioid types), cervical cancers (squamous cell carcinoma in situ,invasive squamous cell carcinoma and endocervical adenocarcinoma),uterine endometrial carcinoma (endometrioid, serous and mucinous types),primary peritoneal carcinoma, mesothelioma (pleura and peritoneum), eyecancer (retinoblastoma), muscle (rhabdosarcoma and leiomyosarcoma),lymphomas, esophageal cancer (adenocarcinoma and squamous cellcarcinoma), gastric cancers (gastric adenocarcinoma and gastrointestinalstroma tumor), liver cancers (hepatocellular carcinoma and bile ductcancer), small intestinal tumors (small intestinal stromal tumor andcarcinoid tumor) colon cancer (adenocarcinoma of the colon, colon highgrade dysplasia and colon carcinoid tumor), and adrenal carcinoma.

Based at least on the observation that certain primary tumors have ahigh IMP3 level (see Examples), determining the presence or levels ofIMP3 in a subject or a biological sample may also be used to determinewhether a subject has or is likely to develop cancer (diagnosticmethod). In one embodiment, a method for determining whether a subjecthas or is likely to develop cancer comprises determining the presence ofIMP3 in the subject, such as in cells or tissues of the subject. Themethod allows the detection or likelihood of development of any cancerthat is associated with high IMP3 expression, as further describedherein. A method may involve measuring levels of IMP3 in a test sampleobtained from a patient having or suspected of having cancer. A methodmay further comprise comparing the observed levels of IMP3 to a controlor to levels of IMP3 found in a normal control sample, for example asample obtained from a subject that does not have cancer. The presenceof IMP3 or the presence of IMP3 at levels that are higher than levelsthat are observed in the normal control indicate the presence of canceror the likelihood of developing cancer. Exemplary cancers include kidneycancer, such as RCC, and urothelial cancers, e.g., superficialurothelial carcinoma of the bladder.

Additionally, disease progression can be assessed by following IMP3levels in individual patients over time. Accordingly, methods providedherein also include methods for monitoring the progression of cancer ina subject, comprising, e.g., monitoring the presence or level of IMP3 ina cell, e.g., in a cancerous cell or tumor, of the subject over time. Anincrease of IMP3 in cancer cells, e.g., over time, indicates that thecancer is progressing. In another embodiment, a reference reading istaken after surgical removal of tissue, e.g., cancerous tissue, thenanother taken at regular intervals. Any rise in IMP3 levels could beindicative of a relapse, or possibly metastasis.

The information provided by the methods described herein may be used bythe physician in determining the most effective course of treatment. Acourse of treatment refers to the therapeutic measures taken for apatient after diagnosis or after treatment for cancer. For example, adetermination of the likelihood for cancer recurrence, spread, orpatient survival, can assist in determining whether a more conservativeor more radical approach to therapy should be taken, or whethertreatment modalities should be combined. For example, when cancerprogression or metastasis is likely, it can be advantageous to precedeor follow surgical treatment with chemotherapy, radiation,immunotherapy, biological modifier therapy, gene therapy, vaccines, andthe like, or adjust the span of time during which the patient istreated.

Also provided herein are methods for treating a subject having cancer. Amethod may comprise (i) determining the presence or level of IMP3 in acancerous tumor of a subject; and (ii) if IMP3 is present or is presentat a higher level in the cancerous tumor of the subject relative to acontrol, treating the subject aggressively, whereas if no IMP3 isdetected or if the level of IMP3 in the cancerous tumor of a subject isstatistically within the range of a control, treating the subject lessaggressively. An aggressive therapy may comprise surgical removal ofcancer cells or a tissue comprising the cancer cells, e.g., nephrectomyin the case of kidney cancer, chemotherapy, radiation, or a combinationthereof. Surgical removal may be followed by early systematic therapy.The treatment may then be followed by monitoring of IMP3 levels.

In one embodiment, a partial or radical nephrectomy or cancer tissueresection is conducted in a subject having a kidney cancer, e.g., RCC,and the presence or level of IMP3 is determined in the tissue, e.g.,tumor tissue obtained by the nephrectomy. If IMP3 is detected in thecancerous tissue, the subject is then treated aggressively, e.g., withpostoperative adjuvant therapy, such as with anti-angiogenic agentsand/or other drugs, e.g., Nexavar® (sorafenib) and Sutent® (sunitinib).If IMP3 is not detected in the cancerous tissue, then the subject may bespared postoperative adjuvant therapy or other aggressive treatment.

IMP3 status in cancer patients, such as in RCC, can be added in thepathology report with other pathological predictors including tumorsize, grade, subtype, and stage for the patient's outcome informationand clinical treatment.

In one embodiment, measuring the presence or level of IMP3 is combinedwith the determination of another prognostic factor, such that thecombined determination results in a more accurate prognosis thendetermining either prognostic factor alone. Other prognostic factorsthat may be determined include tumor stage, size, grade, necrosis,histology type (clear cell, papillary and chromophobe types) and EasternCooperative Oncology Group (ECOG) performance status, and thetumor-node-metastasis (TNM) staging system. In a preferred embodiment, aprognostic method comprises determining the presence or level of IMP3and determining the stage of the tumor. As described in the Examples,the combination of these two prognostic factors provides much betterprognostic information compared with TNM stage alone. For example, thestage and IMP3 level may be compared to the data set forth in thediagram in FIG. 9. This diagram provides that the best to worstdiagnosis are as follows (starting from best to worst): stage 1 and 2RCC with negative IMP3; stage 3 RCC with negative IMP3; stage 1 RCC withlow positive IMP3 and all stage RCC with high positive IMP3 and stage 2and 3 RCC with low positive IMP3. The meaning of “low positive” and“high positive” IMP3 levels is provided in the Examples.

In addition, other prognostic factors for renal cancer, e.g., RCC, whichmay be combined with IMP3 presence of levels include Von Hippel-Linaugene alteration, DNA ploidy, and the following biomarkers: carbonicanhydrase IX (CAIX or CA9), adipose differentiation-related protein(ADFP), p53, mdm2, p27, cyclin A, cyclin D1, PTEN, Ki-67, proliferatingcell nuclear antigen (PCNA); cadherins, catenins, MMP-9,MMP-E2/E-cadherin, CD44, EpCAM, vimentin, MUC1, and immunal regulators(e.g., B7-H1 and B7-H4). These markers are all discussed in Zhong Jiang(2007) Expert Rev. Mol. Diagn. 7:1-15, which is incorporated byreference herein.

Determining the presence or level of IMP3 may also be combined with thedetection of one or more other biomarkers for which increased ordecreased expression correlates with cancer. The selected biomarker canbe a general diagnostic or prognostic marker useful for multiple typesof cancer, such as CA 125, CEA or LDH, or can be a cancer-specificdiagnostic or prognostic marker, such as a colon cancer marker (forexample, sialosyl-TnCEA, CA19-9, or LASA), breast cancer marker (forexample, CA 15-2. Her-2/neu and CA 27.29), ovarian cancer marker (forexample, CA72-4), lung cancer (for example, neuron-specific enolase(NSE) and tissue polypeptide antigen (TPA)), prostate cancer (forexample, PSA, prostate-specific membrane antigen and prostatic acidphosphatase), melanoma (for example, S-100 and TA-90), as well as otherbiomarkers specific for other types of cancer. Those skilled in the artwill be able to select useful diagnostic or prognostic markers fordetection in combination with IMP3. Similarly, three or more, four ormore or five or more or a multitude of biomarkers can be used togetherfor determining a diagnosis or prognosis of a patient.

Also provided herein are kits, e.g., kits for determining the presenceor level of IMP3 in a subject or in a biological sample of a subject. Akit may comprise any agent useful for qualitatively or quantitativelydetecting IMP3 proteins or mRNA (including potentially pre-mRNA), suchas agents further described herein. A kit may further comprise acontrol, such as a control value or control sample or control tissue. Acontrol may be protein or RNA attached to a solid support. A kit mayalso comprise additional components or reagents necessary for thedetection of IMP3, such as secondary antibodies for use inimmunohistochemistry. A kit may further comprise one or more otherbiomarkers or reagents for evaluating other prognostic factors, e.g.,tumor stage.

IMP3 Protein Detection Techniques

Methods for the detection of protein, e.g., IMP3 protein, are well knownto those skilled in the art, and include ELISA (enzyme linkedimmunosorbent assay), RIA (radioimmunoassay), Western blotting, andimmunohistochemistry. Immunoassays such as ELISA or RIA, which can beextremely rapid, are more generally preferred. These methods useantibodies, or antibody equivalents, to detect IMP3 protein. Antibodyarrays or protein chips can also be employed, see for example U.S.Patent Application Nos: 20030013208A1; 20020155493A1, 20030017515 andU.S. Pat. Nos. 6,329,209; 6,365,418, herein incorporated by reference intheir entirety.

ELISA and RIA procedures may be conducted such that a IMP3 standard islabeled (with a radioisotope such as ¹²⁵I or ³⁵S, or an assayableenzyme, such as horseradish peroxidase or alkaline phosphatase), and,together with the unlabelled sample, brought into contact with thecorresponding antibody, whereon a second antibody is used to bind thefirst, and radioactivity or the immobilized enzyme assayed (competitiveassay). Alternatively, IMP3 in the sample is allowed to react with thecorresponding immobilized antibody, radioisotope- or enzyme-labeledanti-IMP3 antibody is allowed to react with the system, andradioactivity or the enzyme assayed (ELISA-sandwich assay). Otherconventional methods may also be employed as suitable.

The above techniques may be conducted essentially as a “one-step” or“two-step” assay. A “one-step” assay involves contacting antigen withimmobilized antibody and, without washing, contacting the mixture withlabeled antibody. A “two-step” assay involves washing before contacting,the mixture with labeled antibody. Other conventional methods may alsobe employed as suitable.

In one embodiment, a method for measuring IMP3 levels comprises thesteps of: contacting a biological specimen with an antibody or variant(e.g., fragment) thereof which selectively binds IMP3, and detectingwhether said antibody or variant thereof is bound to said sample andthereby measuring the levels of IMP3. A method may further comprisecontacting the specimen with a second antibody, e.g., a labeledantibody. The method may further comprise one or more steps of washing,e.g., to remove one or more reagents.

Enzymatic and radiolabeling of IMP3 and/or the antibodies may beeffected by conventional means. Such means will generally includecovalent linking of the enzyme to the antigen or the antibody inquestion, such as by glutaraldehyde, specifically so as not to adverselyaffect the activity of the enzyme, by which is meant that the enzymemust still be capable of interacting with its substrate, although it isnot necessary for all of the enzyme to be active, provided that enoughremains active to permit the assay to be effected. Indeed, sometechniques for binding enzyme are non-specific (such as usingformaldehyde), and will only yield a proportion of active enzyme.

It may be desirable to immobilize one component of the assay system on asupport, thereby allowing other components of the system to be broughtinto contact with the component and readily removed without laboriousand time-consuming labor. It is possible for a second phase to beimmobilized away from the first, but one phase is usually sufficient.

It is possible to immobilize the enzyme itself on a support, but ifsolid-phase enzyme is required, then this is generally best achieved bybinding to antibody and affixing the antibody to a support, models andsystems for which are well-known in the art. Simple polyethylene mayprovide a suitable support.

Enzymes employable for labeling are not particularly limited, but may beselected from the members of the oxidase group, for example. Thesecatalyze production of hydrogen peroxide by reaction with theirsubstrates, and glucose oxidase is often used for its good stability,ease of availability and cheapness, as well as the ready availability ofits substrate (glucose). Activity of the oxidase may be assayed bymeasuring the concentration of hydrogen peroxide formed after reactionof the enzyme-labeled antibody with the substrate under controlledconditions well-known in the art.

Other techniques may be used to detect IMP3 according to apractitioner's preference based upon the present disclosure. One suchtechnique is Western blotting (Towbin et at., Proc. Nat. Acad. Sci.76:4350 (1979)), wherein a suitably treated sample is run on an SDS-PAGEgel before being transferred to a solid support, such as anitrocellulose filter. Anti-IMP3 antibodies (unlabeled) are then broughtinto contact with the support and assayed by a secondary immunologicalreagent, such as labeled protein A or anti-immunoglobulin (suitablelabels including ¹²⁵I, horseradish peroxidase and alkaline phosphatase).Chromatographic detection may also be used.

Immunohistochemistry may be used to detect expression of human IMP3,e.g., in a biopsy sample. A suitable antibody is brought into contactwith, for example, a thin layer of cells, washed, and then contactedwith a second, labeled antibody. Labeling may be by fluorescent markers,enzymes, such as peroxidase, avidin, or radiolabelling. The assay isscored visually, using microscopy. The results may be quantitated, e.g.,as described in the Examples.

As further described in the Examples, immunohistochemical analysisoptionally coupled with quantification of the signal may be conducted asfollows. IMP3 expression may be directly evaluated in the tissue bypreparing immunohistochemically stained slides with, e.g., anavidin-biotinylated peroxidase complex system, as further described inthe Examples. Tumor cells with dark brown color indicate high levels ofIMP3, whereas cells that do not have a detectable level of IMP3 will notappear brown, but rather blue, e.g., if cells are hematoxycilin stained.Accordingly, a subject, e.g., a pathologist, may determine by merelylooking at a slide under a microscope whether cells are brown or not andtherefore whether they contain IMP3, the presence of which would beindicative of a poor prognosis.

Evaluation of the presence of brown stain, i.e., IMP3, may also be doneby quantitative immunohistochemical investigation, e.g., with acomputerized image analyzer (e.g., Automated Cellular Imaging System,ACIS, ChromaVision Medical System Inc., San Juan Capistrano, Calif.) maybe used for evaluation of the levels of IMP3 expression in theimmunostained tissue samples. Using ACIS, “cytoplasmic staining” may bechosen as program for IMP3 detection. Different areas of immunostainedtumor samples may be analyzed with the ACIS system. With ACIS, positivestaining may be calculated by applying two thresholds with onerecognizing blue background (hematoxylin stained) cells and anotherrecognizing brown positive cells. The integrated optical density (IOD)is the sum of pixels times (multiplied by) the intensity of thosepixels. Accordingly, brown IOD is the sum of brown pixels times theintensity of the brown pixels and blue IOD is the sum of blue pixelstimes the intensity of the blue pixels. ACIS values can be calculated asbrown IOD divided by the sum of the blue area and the brown area, i.e.,divided by (blue IOD+brown IOD). An average of the ACIS values that ismore than 1, e.g., about 1.1, 1.2, 1.3, 1.4, 1.5., 2, 2.5, 3, 5, 10, 30,100 or more indicates an elevated IMP3 expression and therefore a poorprognosis.

Other machine or autoimaging systems may also be used to measureimmunostaining results for IMP3. As used herein, “quantitative”immunohistochemistry refers to an automated method of scanning andscoring samples that have undergone immunohistochemistry, to identifyand quantitate the presence of a specified biomarker, such as an antigenor other protein. The score given to the sample is a numericalrepresentation of the intensity of the immunohistochemical staining ofthe sample, and represents the amount of target biomarker present in thesample. As used herein, Optical Density (OD) is a numerical score thatrepresents intensity of staining. As used herein, semi-quantitativeimmunohistochemistry refers to scoring of immunohistochemical results byhuman eye, where a trained operator ranks results numerically (e.g., as1, 2 or 3).

Various automated sample processing, scanning and analysis systemssuitable for use with immunohistochemistry are available in the art.Such systems may include automated staining (see, e.g, the Benchmark™system, Ventana Medical Systems, Inc.) and microscopic scanning,computerized image analysis, serial section comparison (to control forvariation in the orientation and size of a sample), digital reportgeneration, and archiving and tracking of samples (such as slides onwhich tissue sections are placed). Cellular imaging systems arecommercially available that combine conventional light microscopes withdigital image processing systems to perform quantitative analysis oncells and tissues, including immunostained samples. See, e.g., theCAS-200 system (Becton, Dickinson & Co.).

Another method that may be used for detecting and quantitating IMP3protein levels is Western blotting, e.g., as described in the Examples.Tumor tissues may be frozen and homogenized in lysis buffer.Immunodetection can be performed with an IMP3 antibody using theenhanced chemiluminescence system (e.g., from PerkinElmer Life Sciences,Boston, Mass.). The membrane may then be stripped and re-blotted with acontrol antibody, e.g., anti-actin (A-2066) polyclonal antibody fromSigma (St. Louis, Mo.). The intensity of the signal may be quantified bydensitometry software (e.g., NIH Image 1.61). After quantification ofthe IMP3 and control signals (e.g., actin), the relative expressionlevels of IMP3 are normalized by amount of the actin in each lane, i.e.,the value of the IMP3 signal is divided by the value of the controlsignal. IMP3 protein expression is considered to be elevated (andtherefore predictive of a poor prognosis) when the value of IMP3/actinis more than 1, e.g., about 1.1, 1.2, 1.3, 1.4, 1.5., 2, 2.5, 3, 5, 10,30, 100.

Anti-IMP3 antibodies may also be used for imaging purposes, for example,to detect the presence of IMP3 in cells and tissues of a subject.Suitable labels include radioisotopes, iodine (¹²⁵I, ¹²¹I), carbon(¹⁴C), sulphur (³⁵S), tritium (³H), indium (¹¹²In), and technetium(⁹⁹mTc), fluorescent labels, such as fluorescein and rhodamine, andbiotin. Immunoenzymatic interactions can be visualized using differentenzymes such as peroxidase, alkaline phosphatase, or differentchromogens such as DAB, AEC or Fast Red.

For in vivo imaging purposes, antibodies are not detectable, as such,from outside the body, and so must be labeled, or otherwise modified, topermit detection. Markers for this purpose may be any that do notsubstantially interfere with the antibody binding, but which allowexternal detection. Suitable markers may include those that may bedetected by X-radiography, NMR or MRI. For X-radiographic techniques,suitable markers include any radioisotope that emits detectableradiation but that is not overtly harmful to the patient, such as bariumor caesium, for example. Suitable markers for NMR and MRI generallyinclude those with a detectable characteristic spin, such as deuterium,which may be incorporated into the antibody by suitable labeling ofnutrients for the relevant hybridoma, for example.

The size of the subject, and the imaging system used, will determine thequantity of imaging moiety needed to produce diagnostic images. In thecase of a radioisotope moiety, for a human subject, the quantity ofradioactivity injected will normally range from about 5 to 20millicuries of technetium-99 m. The labeled antibody or antibodyfragment will then preferentially accumulate at the location of cellswhich contain IMP3. The labeled antibody or variant thereof, e.g.,antibody fragment, can then be detected using known techniques.

Antibodies that may be used to detect IMP3 include any antibody, whethernatural or synthetic, full length or a fragment thereof, monoclonal orpolyclonal, that binds sufficiently strongly and specifically to theIMP3 to be detected, e.g., human IMP3. An antibody may have a Kd of atmost about 10⁻⁶M, 10⁻⁷M, 10⁻⁸M, 10⁻⁹M, 10⁻¹⁰M, 10⁻¹¹M, 10⁻¹²M. Thephrase “specifically binds” refers to binding of, for example, anantibody to an epitope or antigen or antigenic determinant in such amanner that binding can be displaced or competed with a secondpreparation of identical or similar epitope, antigen or antigenicdeterminant. An antibody may bind preferentially to IMP3 relative toother proteins, such as related proteins, e.g., IMP1 and IMP2.

Antibodies are commercially available, e.g., from DAKO (L523S) or may beprepared according to methods known in the art.

Antibodies and derivatives thereof that may be used encompassespolyclonal or monoclonal antibodies, chimeric, human, humanized,primatized (CDR-grafted), veneered or single-chain antibodies, phaseproduced antibodies (e.g., from phage display libraries), as well asfunctional, i.e., IMP3 binding fragments, of antibodies. For example,antibody fragments capable of binding to IMP3 or portions thereof,including, but not limited to Fv, Fab, Fab′ and F(ab′)₂ fragments can beused. Such fragments can be produced by enzymatic cleavage or byrecombinant techniques. For example, papain or pepsin cleavage cangenerate Fab or F(ab′) 2 fragments, respectively. Other proteases withthe requisite substrate specificity can also be used to generate Fab orF(ab′)₂ fragments. Antibodies can also be produced in a variety oftruncated forms using antibody genes in which one or more stop codonshave been introduced upstream of the natural stop site. For example, achimeric gene encoding a F(ab′)₂ heavy chain portion can be designed toinclude DNA sequences encoding the CH, domain and hinge region of theheavy chain.

Synthetic and engineered antibodies are described in, e.g., Cabilly etal., U.S. Pat. No. 4,816,567 Cabilly et al., European Patent No.0,125,023 B1; Boss et al., U.S. Pat. No. 4,816,397; Boss et al.,European Patent No. 0,120,694 B1; Neuberger, M. S. et al., WO 86/01533;Neuberger, M. S. et al., European Patent No. 0,194,276 B1; Winter, U.S.Pat. No. 5,225,539; Winter, European Patent No. 0,239,400 B1; Queen etal., European Patent No. 0451216 B1; and Padlan, E. A. et al., EP0519596 A1. See also, Newman, R. et al., BioTechnology, 10: 1455-1460(1992), regarding primatized antibody, and Ladner et al., U.S. Pat. No.4,946,778 and Bird, R. E. et al., Science, 242: 423-426 (1988))regarding single-chain antibodies.

In some embodiments, agents that specifically bind to IMP3 other thanantibodies are used, such as peptides. Peptides that specifically bindto IMP3 can be identified by any means known in the art. For example,specific peptide binders of IMP3 can be screened for using peptide phagedisplay libraries.

Generally, an agent that is capable of detecting an IMP3 polypeptide,such that the presence of IMP3 is detected and/or quantitated, may beused. As defined herein, an “agent” refers to a substance that iscapable of identifying or detecting IMP3 in a biological sample (e.g.,identifies or detects IMP3 mRNA, IMP3 DNA, IMP3 protein). In oneembodiment, the agent is a labeled or labelable antibody whichspecifically binds to IMP3 polypeptide. As used herein, the phrase“labeled or labelable” refers to the attaching or including of a label(e.g., a marker or indicator) or ability to attach or include a label(e.g., a marker or indicator). Markers or indicators include, but arenot limited to, for example, radioactive molecules, colorimetricmolecules, and enzymatic molecules which produce detectable changes in asubstrate.

In addition, an IMP3 protein may be detected using Mass Spectrometrysuch as MALDI/TOF (time-of-flight), SELDI/TOF, liquidchromatography-mass spectrometry (LC-MS), gas chromatography-massspectrometry (GC-MS), high performance liquid chromatography-massspectrometry (HPLC-MS), capillary electrophoresis-mass spectrometry,nuclear magnetic resonance spectrometry, or tandem mass spectrometry(e.g., MS/MS, MS/MS/MS, ESI-MS/MS, etc.). See for example, U.S. PatentApplication Nos: 20030199001, 20030134304, 20030077616, which are hereinincorporated by reference.

Mass spectrometry methods are well known in the art and have been usedto quantify and/or identify biomolecules, such as proteins (see, e.g.,Li et al. (2000) Tibtech 18:151-160; Rowley et al. (2000) Methods 20:383-397; and Kuster and Mann (1998) Curr. Opin. Structural Biol. 8:393-400). Further, mass spectrometric techniques have been developedthat permit at least partial de novo sequencing of isolated proteins.Chait et al., Science 262:89-92 (1993); Keough et al., Proc. Natl. Acad.Sci. USA. 96:7131-6 (1999); reviewed in Bergman, EXS 88:133-44 (2000).

In certain embodiments, a gas phase ion spectrophotometer is used. Inother embodiments, laser-desorption/ionization mass spectrometry is usedto analyze the sample. Modem laser desorption/ionization massspectrometry (“LDI-MS”) can be practiced in two main variations: matrixassisted laser desorption/ionization (“MALDI”) mass spectrometry andsurface-enhanced laser desorption/ionization (“SELDI”). In MALDI, theanalyte is mixed with a solution containing a matrix, and a drop of theliquid is placed on the surface of a substrate. The matrix solution thenco-crystallizes with the biological molecules. The substrate is insertedinto the mass spectrometer. Laser energy is directed to the substratesurface where it desorbs and ionizes the biological molecules withoutsignificantly fragmenting them. However, MALDI has limitations as ananalytical tool. It does not provide means for fractionating the sample,and the matrix material can interfere with detection, especially for lowmolecular weight analytes. See, e.g., U.S. Pat. No. 5,118,937(Hillenkamp et al.), and U.S. Pat. No. 5,045,694 (Beavis & Chait).

In SELDI, the substrate surface is modified so that it is an activeparticipant in the desorption process. In one variant, the surface isderivatized with adsorbent and/or capture reagents that selectively bindthe protein of interest. In another variant, the surface is derivatizedwith energy absorbing molecules that are not desorbed when struck withthe laser. In another variant, the surface is derivatized with moleculesthat bind the protein of interest and that contain a photolytic bondthat is broken upon application of the laser. In each of these methods,the derivatizing agent generally is localized to a specific location onthe substrate surface where the sample is applied. See, e.g., U.S. Pat.No. 5,719,060 (Hutchens & Yip) and WO 98/59361 (Hutchens & Yip). The twomethods can be combined by, for example, using a SELDI affinity surfaceto capture an analyte and adding matrix-containing liquid to thecaptured analyte to provide the energy absorbing material.

For additional information regarding mass spectrometers, see, e.g.,Principles of Instrumental Analysis, 3rd edition., Skoog, SaundersCollege Publishing, Philadelphia, 1985; and Kirk-Othmer Encyclopedia ofChemical Technology, 4.sup.th ed. Vol. 15 (John Wiley & Sons, New York1995), pp. 1071-1094.

Detection of the presence of a marker or other substances will typicallyinvolve detection of signal intensity. This, in turn, can reflect thequantity and character of a polypeptide bound to the substrate. Forexample, in certain embodiments, the signal strength of peak values fromspectra of a first sample and a second sample can be compared (e.g.,visually, by computer analysis etc.), to determine the relative amountsof particular biomolecules. Software programs such as the BiomarkerWizard program (Ciphergen Biosystems, Inc., Fremont, Calif.) can be usedto aid in analyzing mass spectra. The mass spectrometers and theirtechniques are well known to those of skill in the art.

Any person skilled in the art understands, any of the components of amass spectrometer (e.g., desorption source, mass analyzer, detect, etc.)and varied sample preparations can be combined with other suitablecomponents or preparations described herein, or to those known in theart. For example, in some embodiments a control sample may contain heavyatoms (e.g. ¹³C) thereby permitting the test sample to be mixed with theknown control sample in the same mass spectrometry run.

In one preferred embodiment, a laser desorption time-of-flight (TOF)mass spectrometer is used. In laser desorption mass spectrometry, asubstrate with a bound marker is introduced into an inlet system. Themarker is desorbed and ionized into the gas phase by laser from theionization source. The ions generated are collected by an ion opticassembly, and then in a time-of-flight mass analyzer, ions areaccelerated through a short high voltage field and let drift into a highvacuum chamber. At the far end of the high vacuum chamber, theaccelerated ions strike a sensitive detector surface at a differenttime. Since the time-of-flight is a function of the mass of the ions,the elapsed time between ion formation and ion detector impact can beused to identify the presence or absence of molecules of specific massto charge ratio.

In some embodiments the relative amounts of one or more biomoleculespresent in a first or second sample is determined, in part, by executingan algorithm with a programmable digital computer. The algorithmidentifies at least one peak value in the first mass spectrum and thesecond mass spectrum. The algorithm then compares the signal strength ofthe peak value of the first mass spectrum to the signal strength of thepeak value of the second mass spectrum of the mass spectrum. Therelative signal strengths are an indication of the amount of thebiomolecule that is present in the first and second samples. A standardcontaining a known amount of a biomolecule can be analyzed as the secondsample to better quantify the amount of the biomolecule present in thefirst sample. In certain embodiments, the identity of the biomoleculesin the first and second sample can also be determined.

IMP3 RNA Detection Techniques

Any method for qualitatively or quantitatively detecting IMP3 RNA, e.g.,mRNA, may be used.

Detection of RNA transcripts may be achieved by Northern blotting, forexample, wherein a preparation of RNA is run on a denaturing agarosegel, and transferred to a suitable support, such as activated cellulose,nitrocellulose or glass or nylon membranes. Radiolabeled cDNA or RNA isthen hybridized to the preparation, washed and analyzed byautoradiography.

Detection of RNA transcripts can further be accomplished usingamplification methods. For example, it is within the scope of thepresent invention to reverse transcribe mRNA into cDNA followed bypolymerase chain reaction (RT-PCR); or, to use a single enzyme for bothsteps as described in U.S. Pat. No. 5,322,770, or reverse transcribemRNA into cDNA followed by symmetric gap ligase chain reaction(RT-AGLCR) as described by R. L. Marshall, et al., PCR Methods andApplications 4: 80-84 (1994).

In one embodiment, quantitative real-time polymerase chain reaction(qRT-PCR) is used to evaluate mRNA levels of IMP3 (see Examples). IMP3and a control mRNA, e.g., glyceraldehyde-3-phosphate dehydrogenase(GAPDH) mRNA levels may be quantitated in cancer tissue and adjacentbenign tissues. For this, frozen tissues may be cut into 5 micronsections and total RNA may be extracted, e.g., by Qiagen RNeasy Mini Kit(Qiagen, Inc., Valencia, Calif.). A certain amount of RNA, e.g., fivehundred nanograms of total RNA, from each tissue may be reverselytranscribed by using, e.g., Qiagen Omniscript RT Kit. Two-step qRT-PCRmay be performed, e.g., with the ABI TaqMan PCR reagent kit (ABI Inc,Foster City, Calif.), and IMP3 primers and GAPDH primers, and the probesfor both genes on ABI Prism 7700 system. The primers that may be usedare set forth in the Examples. The IMP3 copy number may then be dividedby the GAPDH copy number and multiplied by 1,000 to give a value for theparticular subject. In other words, the amount of IMP3 mRNA wasnormalized with the amount of GAPDH mRNA measured in the same RNAextraction to obtain an IMP3/GAPDH ratio. A ratio that is equal to ormore than 1, e.g., about 1.1, 1.2, 1.3, 1.4, 1.5., 2, 2.5, 3, 5, 10, 30,100 may be considered as a high IMP3 expression and therefore a poorprognosis.

Other known amplification methods which can be utilized herein includebut are not limited to the so-called “NASBA” or “3SR” techniquedescribed in PNAS USA 87: 1874-1878 (1990) and also described in Nature350 (No. 6313): 91-92 (1991); Q-beta amplification as described inpublished European Patent Application (EPA) No. 4544610; stranddisplacement amplification (as described in G. T. Walker et al., Clin.Chem. 42: 9-13 (1996) and European Patent Application No. 684315; andtarget mediated amplification, as described by PCT PublicationWO9322461.

Primers that may be used for amplification of IMP3 nucleic acid portionsare set forth in the Examples.

In situ hybridization visualization may also be employed, wherein aradioactively labeled antisense RNA probe is hybridized with a thinsection of a biopsy sample, washed, cleaved with RNase and exposed to asensitive emulsion for autoradiography. The samples may be stained withhaematoxylin to demonstrate the histological composition of the sample,and dark field imaging with a suitable light filter shows the developedemulsion. Non-radioactive labels such as digoxigenin may also be used.

Another method for evaluation of IMP3 expression is to detect geneamplification by fluorescent in situ hybridization (FISH). FISH is atechnique that can directly identify a specific region of DNA or RNA ina cell and therefore enables to visual determination of the IMP3expression in tissue samples. The FISH method has the advantages of amore objective scoring system and the presence of a built-in internalcontrol consisting of the IMP3 gene signals present in allnon-neoplastic cells in the same sample. Fluorescence in situhybridization is a direct in situ technique that is relatively rapid andsensitive. FISH test also can be automated. Immunohistochemistry can becombined with a FISH method when the expression level of IMP3 isdifficult to determine by immunohistochemistry alone.

Alternatively, mRNA expression can be detected on a DNA array, chip or amicroarray. Oligonucleotides corresponding to the IMP3 are immobilizedon a chip which is then hybridized with labeled nucleic acids of a testsample obtained from a patient. Positive hybridization signal isobtained with the sample containing IMP3 transcripts. Methods ofpreparing DNA arrays and their use are well known in the art. (See, forexample U.S. Pat. Nos. 6,618,6796; 6,379,897; 6,664,377; 6,451,536;548,257; U.S. 20030157485 and Schena et al. 1995 Science 20:467-470;Gerhold et al. 1999 Trends in Biochem. Sci. 24, 168-173; and Lennon etal. 2000 Drug discovery Today 5: 59-65, which are herein incorporated byreference in their entirety). Serial Analysis of Gene Expression (SAGE)can also be performed (See for example U.S. Patent Application20030215858).

To monitor mRNA levels, for example, mRNA is extracted from thebiological sample to be tested, reverse transcribed, andfluorescent-labeled cDNA probes are generated. The microarrays capableof hybridizing to IMP3 cDNA are then probed with the labeled cDNAprobes, the slides scanned and fluorescence intensity measured. Thisintensity correlates with the hybridization intensity and expressionlevels.

Types of probes for detection of IMP3 RNA include cDNA, riboprobes,synthetic oligonucleotides and genomic probes. The type of probe usedwill generally be dictated by the particular situation, such asriboprobes for in situ hybridization, and cDNA for Northern blotting,for example. Most preferably, the probe is directed to nucleotideregions unique to IMP3 RNA. The probes may be as short as is required todifferentially recognize IMP3 mRNA transcripts, and may be as short as,for example, 15 bases; however, probes of at least 17 bases, morepreferably 18 bases and still more preferably 20 bases are preferred.Preferably, the primers and probes hybridize specifically understringent conditions to a DNA fragment having the nucleotide sequencecorresponding to the IMP3 gene. As herein used, the term “stringentconditions” means hybridization will occur only if there is at least 95%and preferably at least 97% identity between the sequences.

The form of labeling of the probes may be any that is appropriate, suchas the use of radioisotopes, for example, ³²P and ³⁵S. Labeling withradioisotopes may be achieved, whether the probe is synthesizedchemically or biologically, by the use of suitably labeled bases.

IMP3 Autoantibody Detection

In one embodiment, the level of IMP3 in a subject is determined by thelevel of IMP3 autoantibodies. An exemplary method comprises determiningthe presence of IMP3 autoantibodies in a subject, such as in a bodilyfluid or sample of the subject, wherein the presence of IMP3autoantibodies in the bodily fluid or sample of the subject, indicatesthat the subject has a poor prognosis. In another embodiment, the methodcomprises determining the level of IMP3 autoantibodies in a subject;comparing the level of autoantibodies to that in a control, e.g., asubject who does not have a cancer, and optionally to that of one ormore subjects who have a cancer, e.g., a slow progressive cancer or aninvasive cancer and/or a cancer having a high likelihood of metastasis;and or a poor or a good prognosis. A higher level of IMP3 autoantibodiesmay be a level that is statistically significant, e.g., at least about1.1, 1.2, 1.3, 1.4, 1.5., 2, 2.5, 3, 5, 10, 30, 100 times higher.

Human tumors stimulate the production of autoantibodies againstautologous cellular proteins called tumor associated antigens (TAAs)(see, e.g., Wang et al. New England J. Med. (2005) 353:1224 and Int. J.Oncol. (2005) 26:311). The level of IMP3 autoantibodies may be detectedand/or measured in a bodily fluid of a subject, e.g., in blood or serum.Antibodies may be detected by spectrometry, ELISA, PCR, cDNA, peptidephage display, autoantigen microarray, immunoblotting (see, e.g.,Casiano et al. (May 2006) Mol. Cell. Proteomics). In one embodiment, anIMP3 protein or one or more peptide thereof is used as an agent todetect IMP3 antibodies.

Therapeutic Applications Using IMP3

Based at least on the observation that high IMP3 levels in primarytumors is associated with a higher likelihood of metastasis and a poorprognosis, it may be possible to prevent the likelihood of metastasisand progression of the cancer or prevent cancer altogether by inhibitingor reducing the expression level of IMP3 or IMP3 activity in the tumoror tissue of the subject. In particular, recent studies havedemonstrated that IMP3 promotes tumor cell proliferation and invasion(Liao et al. (2006) J. Biol. Chem. 280:18517 and Vikesaa et al. (2006)EMBO J. 25:1456). In one embodiment, a method for treating or preventingcancer, such as kidney or a urogenital cancer, comprises reducing thelevel of expression of IMP3, reducing the amount of IMP3 protein, orinhibiting the activity of an IMP3 protein. In a method for treatment ofcancer, one may reduce IMP3 levels or activity in a tumor, e.g., aprimary tumor. In a method for preventing cancer, one may reduce IMP3levels or activity in tissue likely to develop cancer, e.g., tissue thatexhibits high levels of IMP3 expression.

Prophylaxis may be appropriate even at very early stages of the disease,to prevent metastasis. Thus, administration of an agent that reducesIMP3 levels or activity may be effected as soon as cancer is diagnosed,and treatment continued for as long as is necessary, preferably untilthe threat of the disease has been removed. Such treatment may also beused prophylactically in individuals at high risk for development ofcertain cancers, e.g., prostate or breast.

RNAi Technology

In one embodiment, IMP3 levels are decreased by administration of orexpression in a subject, e.g., in cells or a tissue of the subject, ofone or more IMP3 siRNAs.

The term “short interfering RNAs (siRNA)” as used herein is intended torefer to any nucleic acid molecule capable of mediating RNAi or genesilencing. The term siRNA is intended to encompass various naturallygenerated or synthetic compounds, with RNAi function. Such compoundsinclude, without limitation, duplex synthetic oligonucleotides, of about21 to 23 base pairs with terminal overlaps of 2 or 3 base pairs; hairpinstructures of one oligonucleotide chain with sense and complementary,hybridizing, segments of 21-23 base pairs joined by a loop of, e.g., 3-5base pairs; and various genetic constructs leading to the expression ofthe preceding structures or functional equivalents. Such geneticconstructs are usually prepared in vitro and introduced in the testsystem, but can also include siRNA from naturally occurring siRNAprecursors coded by the genome of the host cell or animal.

It is not a requirement that the siRNA be comprised solely of RNA. Inone embodiment, the siRNA comprises one or more chemical modificationsand/or nucleotide analogues. The modification and/or analogue may be anymodification and/or analogue, respectively, that does not negativelyaffect the ability of the siRNA to inhibit IMP3 expression. Theinclusion of one or more chemical modifications and/or nucleotideanalogues in an siRNA may be preferred to prevent or slow nucleasedigestion, and in turn, create a more stable siRNA for practical use.Chemical modifications and/or nucleotide analogues which stabilize RNAare known in the art. Phosphorothioate derivatives, which include thereplacement of non-bridging phosphoroyl oxygen atoms with sulfur atoms,are one example of analogues showing increased resistance to nucleasedigestion. Sites of the siRNA which may be targeted for chemicalmodification include the loop region of a hairpin structure, the 5′ and3′ ends of a hairpin structure (e.g. cap structures), the 3′ overhangregions of a double-stranded linear siRNA, the 5′ or 3′ ends of thesense strand and/or antisense strand of a linear siRNA, and one or morenucleotides of the sense and/or antisense strand.

As used herein, the term siRNA is intended to be equivalent to any termin the art defined as a molecule capable of mediating sequence-specificRNAi. Such equivalents include, for example, double-stranded RNA(dsRNA), micro-RNA (mRNA), short hairpin RNA (shRNA), short interferingoligonucleotide, and post-transcriptional gene silencing RNA (ptgsRNA).

siRNAs may be introduced into cells to suppress gene expression fortherapeutic or prophylactic purposes as described in InternationalPublication Number WO 0175164. Publications describing RNAi technologyinclude but are not limited to the following: U.S. Pat. No. 6,686,463,U.S. Pat. No. 6,673,611, U.S. Pat. No. 6,623,962, U.S. Pat. No.6,506,559, U.S. Pat. No. 6,573,099, and U.S. Pat. No. 6,531,644; U.S.publication Nos: 20030153519, 20030167490, International PublicationNumbers WO04061081; WO04052093; WO04048596; WO04048594; WO04048581;WO04048566; WO04046320; WO04044537; WO04043406; WO04033620; WO04030660;WO04028471; WO 0175164. Papers which describe the methods and conceptsfor the optimal use of these compounds include but are not limited tothe following: Brummelkamp Science 296: 550-553 (2002); Caplen ExpertOpin. Biol. Ther. 3:575-86 (2003); Brummelkamp, Sciencexpress 21 Mar. 31-6 (2003); Yu Proc Natl Acad Sci USA 99:6047-52 (2002); Paul NatureBiotechnology 29:505-8 (2002); Paddison Proc Natl Acad Sci USA 99:1443-8(2002); Brummelkamp Nature 424: 797-801 (2003); Brummelkamp, Science296: -550-3 (2003); Sui Proc Natl Acad Sci USA 99: 5515-20 (2002);Paddison, Genes and Development 16:948-58 (2002).

A composition comprising an siRNA effective to inhibit IMP3 expressionmay include an RNA duplex comprising a sense sequence of IMP3. In thisembodiment, the RNA duplex comprises a first strand comprising a sensesequence of IMP3 and a second strand comprising a reverse complement ofthe sense sequence of IMP3. In one embodiment the sense sequence of IMP3comprises of from 10 to 25 nucleotides in length. More preferably, thesense sequence of IMP3 comprises of from 19 to 25 nucleotides in length.Most preferably, the sense sequence of IMP3 comprises of from 21 to 23nucleotides in length. The sense sequence of IMP3 preferably comprises asequence of IMP3 containing a translational start site, and may comprisea portion of IMP3 sequence within the first 400 nt of the human IMP3mRNA.

In another embodiment, a composition comprising an siRNA effective toinhibit IMP3 expression may comprise in a single molecule a sensesequence of IMP3, the reverse complement of the sense sequence of IMP3,and an intervening sequence enabling duplex formation between the senseand reverse complement sequences. The sense sequence of IMP3 maycomprise 10 to 25 nucleotides in length, or more preferably 19 to 25nucleotides in length, or most preferably 21 to 23 nucleotides inlength.

It will be readily apparent to one of skill in the art that an siRNA ofthe present invention may comprise a sense sequence of IMP3 or thereverse complement of the sense sequence of IMP3 which is less thanperfectly complementary to each other or to the targeted region of IMP3.In other words, the siRNA may comprise mismatches or bulges within thesense or reverse complement sequence. In one aspect, the sense sequenceor its reverse complement may not be entirely contiguous. The sequenceor sequences may comprise one or more substitutions, deletions, and/orinsertions. The only requirement of the present invention is that thesiRNA sense sequence possess enough complementarity to its reversecomplement and to the targeted region of IMP3 to allow for RNAiactivity. It is an object of the present invention, therefore, toprovide for sequence modifications of an siRNA of the present inventionthat retain sufficient complementarity to allow for RNAi activity. Oneof skill in the art may predict that a modified siRNA composition of thepresent invention will work based on the calculated binding free energyof the modified sequence for the complement sequence and targeted regionof IMP3. Calculation of binding free energies for nucleic acids and theeffect of such values on strand hybridization is known in the art.

A wide variety of delivery systems are available for use in deliveringan siRNA to a target cell in vitro and in vivo. An siRNA of the presentinvention may be introduced directly or indirectly into a cell in whichIMP3 inhibition is desired. An siRNA may be directly introduced into acell by, for example, injection. As such, it is an object of theinvention to provide for a composition comprising an siRNA effective toinhibit IMP3 in injectable, dosage unit form. An siRNA of the presentinvention may be injected intravenously or subcutaneously as an example,for therapeutical use in conjunction with the methods and compositionsof the present invention. Such treatment may include intermittent orcontinuous administration until therapeutically effective levels areachieved to inhibit IMP3 expression in the desired tissue.

Indirectly, an expressible DNA sequence or sequences encoding the siRNAmay be introduced into a cell, and the siRNA thereafter transcribed fromthe DNA sequence or sequences. It is an object of the present invention,therefore, to provide for compositions comprising a DNA sequence orsequences which encode an siRNA effective to inhibit IMP3 expression.

A DNA composition of the present invention comprises a first DNAsequence which encodes a first RNA sequence comprising a sense sequenceof IMP3 and a second DNA sequence which encodes a second RNA sequencecomprising the reverse complement of the sense sequence of IMP3. Thefirst and second RNA sequences, when hybridized, form an siRNA duplexcapable of forming an RNA-induced silencing complex, the RNA-inducedsilencing complex being capable of inhibiting IMP3 expression. The firstand second DNA sequences may be chemically synthesized or synthesized byPCR using appropriate primers to IMP3. Alternatively, the DNA sequencesmay be obtained by recombinant manipulation using cloning technology,which is well known in the art. Once obtained, the DNA sequences may bepurified, combined, and then introduced into a cell in which IMP3inhibition is desired. Alternatively, the sequences may be contained ina single vector or separate vectors, and the vector or vectorsintroduced into the cell in which IMP3 inhibition is desired.

Delivery systems available for use in delivering a DNA composition ofthe present invention to a target cell include, for example, viral andnon-viral systems. Examples of suitable viral systems include, forexample, adenoviral vectors, adeno-associated virus, lentivirus,poxvirus, retroviral vectors, vaccinia, herpes simplex virus, HIV, theminute virus of mice, hepatitis B virus and influenza virus. Non-viraldelivery systems may also be used, for example using, uncomplexed DNA,DNA-liposome complexes, DNA-protein complexes and DNA-coated goldparticles, bacterial vectors such as salmonella, and other technologiessuch as those involving VP22 transport protein, Co-X-gene, and repliconvectors. A viral or non-viral vector in the context of the presentinvention may express the antigen of interest.

Antisense Technology

In another embodiment, the level of IMP3 is reduced or decreased byadministration or the expression of antisense molecules in a subject ortissue or cell thereof.

Gene expression can be controlled through triple-helix formation orantisense DNA or RNA, both of which methods are based on binding of apolynucleotide to DNA or RNA. An antisense nucleic acid molecule whichis complementary to a nucleic acid molecule encoding IMP3 can bedesigned based on the known IMP3 nucleotide sequences. An antisensenucleic acid molecule can comprise a nucleotide sequence which iscomplementary to a coding strand of a nucleic acid, e.g. complementaryto an mRNA sequence, constructed according to the rules of Watson andCrick base pairing, and can hydrogen bond to the coding strand of thenucleic acid. The antisense sequence complementary to a sequence of anmRNA can be complementary to a sequence in the coding region of the mRNAor can be complementary to a 5′ or 3′ untranslated region of the mRNA.Furthermore, an antisense nucleic acid can be complementary in sequenceto a regulatory region of the gene encoding the mRNA, for instance atranscription initiation sequence or regulatory element. Preferably, anantisense nucleic acid complementary to a region preceding or spanningthe initiation codon or in the 3′ untranslated region of an mRNA isused. A nucleic acid is designed which has a sequence complementary to asequence of the coding or untranslated region of the shown nucleic acid.Alternatively, an antisense nucleic acid can be designed based uponsequences of the IMP3 gene, which are known or can be identified byscreening a genomic DNA library with an isolated nucleic acid of theinvention. For example, the sequence of an important regulatory elementcan be determined by standard techniques and a sequence which isantisense to the regulatory element can be designed.

The antisense nucleic acids and oligonucleotides of the invention can beconstructed using chemical synthesis and enzymatic ligation reactionsusing procedures known in the art. The antisense nucleic acid oroligonucleotide can be chemically synthesized using naturally occurringnucleotides or variously modified nucleotides designed to increase thebiological stability of the molecules or to increase the physicalstability of the duplex formed between the antisense and sense nucleicacids e.g. phosphorothioate derivatives and acridine substitutednucleotides can be used. Alternatively, the antisense nucleic acids andoligonucleotides can be produced biologically using an expression vectorinto which a nucleic acid has been subcloned in an antisense orientation(i.e. nucleic acid transcribed from the inserted nucleic acid will be ofan antisense orientation to a target nucleic acid of interest). Theantisense expression vector is introduced into cells in the form of arecombinant plasmid, phagemid or attenuated virus in which antisensenucleic acids are produced under the control of a high efficiencyregulatory region, the activity of which can be determined by the celltype into which the vector is introduced. For a discussion of theregulation of gene expression using antisense genes see Weintraub, H. etal., Antisense RNA as a molecular tool for genetic analysis,Reviews—Trends in Genetics, Vol. 1 (1)1986.

In addition, ribozymes can be used to inhibit expression of IMP3. Forexample, the nucleic acids of the invention can further be used todesign ribozymes which are capable of cleaving a single-stranded nucleicacid encoding a IMP3 protein, such as a IMP3 mRNA transcript. Acatalytic RNA (ribozyme) having ribonuclease activity can be designedwhich has specificity for an mRNA encoding IMP3 based upon the sequenceof a nucleic acid of the invention. For example, a derivative of aTetrahymena L-19 IVS RNA can be constructed in which the base sequenceof the active site is complementary to the base sequence to be cleavedin a IMP3-encoding mRNA. See for example Cech, et al., U.S. Pat. No.4,987,071; Cech, et al., U.S. Pat. No. 5,116,742. Alternatively, anucleic acid of the invention could be used to select a catalytic RNAhaving a specific ribonuclease activity from a pool of RNA molecules.See for example Bartel, D. and Szostak, J. W. Science 261: 1411-1418(1993). RNA-mediated interference (RNAi) (Fire, et al., Nature 391:806-811, 1998) may also be used.

IMP3 Blocking Antibodies and Aptamers

In yet another embodiment, IMP3 levels are reduced by administration toor expression in a subject or a cell or tissue thereof, of IMP3 blockingantibodies or aptamers.

Antibodies, or their equivalents and derivatives, e.g., intrabodies, orother IMP3 antagonists may be used in accordance with the presentinvention for the treatment or prophylaxis of cancers. Administration ofa suitable dose of the antibody or the antagonist may serve to block theactivity of the protein and this may provide a crucial time window inwhich to treat the malignant growth.

A method of treatment may involve attachment of a suitable toxin to IMP3antibodies which then target the area of the tumor. Such toxins are wellknown in the art, and may comprise toxic radioisotopes, heavy metals,enzymes and complement activators, as well as such natural toxins asricin which are capable of acting at the level of only one or twomolecules per cell. It may also be possible to use such a technique todeliver localized doses of suitable physiologically active compounds,which may be used, for example, to treat cancers.

The antibody (or other inhibitors or intrabody) can be administered by anumber of methods. One preferred method is set forth by Marasco andHaseltine in PCT WO94/02610, which is incorporated herein by reference.This method discloses the intracellular delivery of a gene encoding theantibody. One would preferably use a gene encoding a single chainantibody. The antibody would preferably contain a nuclear localizationsequence. One preferably uses an SV40 nuclear localization signal. Bythis method one can intracellularly express an antibody, which can blockIMP3 functioning in desired cells.

Where the present invention provides for the administration of, forexample, antibodies to a patient, then this may be by any suitableroute. If the tumor is still thought to be, or diagnosed as, localized,then an appropriate method of administration may be by injection directto the site. Administration may also be by injection, includingsubcutaneous, intramuscular, intravenous and intradermal injections.

Aptamers can be produced using the methodology disclosed in a U.S. Pat.No. 5,270,163 and WO 91/19813.

Other IMP3 Inhibitors

Other agents, e.g., compounds, that inhibit the activity of IMP3 mayalso be used. Such compounds include small molecules, e.g., moleculesthat interact with the active site or a binding site of the protein,e.g., an RNA binding site. For example, an IMP3 inhibitory agent may bean agent that inhibits binding of IMP3 to its target mRNA. One agentthat can be used is a target RNA or a portion thereof to which IMP3binds. In one embodiment, a large amount of such an oligonucleotide ornucleic acid is administered to a subject to thereby prevent IMP3 toreach its targets in the cell, and thereby prevent IMP3 activity. Anagent may be a portion of IGF-II mRNA to which IMP3 binds, such as aportion of an IGF-II leader 3 mRNA (see, e.g., Nielsen et al. Scand JClin Lab Invest Suppl. 2001; 234:93). Other agents may be identifiedaccording to methods known in the art.

Pharmaceutical Compositions

Formulations may be any that are appropriate to the route ofadministration, and will be apparent to those skilled in the art. Theformulations may contain a suitable carrier, such as saline, and mayalso comprise bulking agents, other medicinal preparations, adjuvantsand any other suitable pharmaceutical ingredients. Catheters are onepreferred mode of administration.

The term “pharmaceutically acceptable” refers to compounds andcompositions which may be administered to mammals without unduetoxicity. Exemplary pharmaceutically acceptable salts include mineralacid salts such as hydrochlorides, hydrobromides, phosphates, sulfates,and the like; and the salts of organic acids such as acetates,propionates, malonates, benzoates, and the like.

The antibodies, nucleic acids or antagonists of the invention may beadministered orally, topically, or by parenteral means, includingsubcutaneous and intramuscular injection, implantation of sustainedrelease depots, intravenous injection, intranasal administration, andthe like. Accordingly, antibodies or nucleic acids of the invention maybe administered as a pharmaceutical composition comprising the antibodyor nucleic acid of the invention in combination with a pharmaceuticallyacceptable carrier. Such compositions may be aqueous solutions,emulsions, creams, ointments, suspensions, gels, liposomal suspensions,and the like. Suitable carriers (excipients) include water, saline,Ringer's solution, dextrose solution, and solutions of ethanol, glucose,sucrose, dextran, mannose, mannitol, sorbitol, polyethylene glycol(PEG), phosphate, acetate, gelatin, collagen, Carbopol Registered TM,vegetable oils, and the like. One may additionally include suitablepreservatives, stabilizers, antioxidants, antimicrobials, and bufferingagents, for example, BHA, BHT, citric acid, ascorbic acid, tetracycline,and the like. Cream or ointment bases useful in formulation includelanolin, Silvadene® (Marion), Aquaphor® (Duke Laboratories), and thelike. Other topical formulations include aerosols, bandages, and otherwound dressings. Alternatively one may incorporate or encapsulate thecompounds in a suitable polymer matrix or membrane, thus providing asustained-release delivery device suitable for implantation near thesite to be treated locally. Other devices include indwelling cathetersand devices such as the Alzet® minipump. Ophthalmic preparations may beformulated using commercially available vehicles such as Sorbi-care®(Allergan), Neodecadron® (Merck, Sharp & Dohme), Lacrilube®, and thelike, or may employ topical preparations such as that described in U.S.Pat. No. 5,124,155. Further, one may provide an antagonist in solidform, especially as a lyophilized powder. Lyophilized formulationstypically contain stabilizing and bulking agents, for example humanserum albumin, sucrose, mannitol, and the like. A thorough discussion ofpharmaceutically acceptable excipients is available in Remington'sPharmaceutical Sciences (Mack Pub. Co.).

The amount of antibody, nucleic acid or inhibitor required to treat anyparticular disorder will of course vary depending upon the nature andseverity of the disorder, the age and condition of the subject, andother factors readily determined by one of ordinary skill in the art.

Immunotherapy

In further aspects, the present invention provides methods for usingIMP3 or an immunoreactive polypeptide thereof (or DNA encoding theprotein or polypeptides) for immunotherapy of cancer in a patient.Accordingly, IMP3 or an immunoreactive polypeptide thereof may be usedto treat cancer or to inhibit the development of cancer.

In accordance with this method, the protein, polypeptide or DNA isgenerally present within a pharmaceutical composition and/or a vaccine.Pharmaceutical compositions may comprise the full length protein or oneor more immunogenic polypeptides, and a physiologically acceptablecarrier. The vaccines may comprise the full length protein or one ormore immunogenic polypeptides and a non-specific immune responseenhancer, such as an adjuvant, biodegradable microsphere (PLG) or aliposome (into which the polypeptide is incorporated).

Alternatively, a pharmaceutical composition or vaccine may contain DNAencoding IMP3 or an immunogenic polypeptide thereof, such that the fulllength protein or polypeptide is generated in situ. In suchpharmaceutical compositions and vaccines, the DNA may be present withinany of a variety of delivery systems known to those of ordinary skill inthe art, including nucleic acid expression systems, bacteria and viralexpression systems. Appropriate nucleic acid expression systems containthe necessary DNA sequences for expression in the patient (such as asuitable promoter). Bacterial delivery systems involve theadministration of a bacterium (such as Bacillus-Calmette-Guerrin) thatexpresses an epitope of a prostate cell antigen on its cell surface. Ina preferred embodiment, the DNA may be introduced using a viralexpression system (e.g., vaccinia or other pox virus, retrovirus, oradenovirus), which may involve the use of a non-pathogenic (defective),replication competent virus. Suitable systems are disclosed, forexample, in Fisher-Hoch et al., PNAS 86:317-321, 1989; Flexner et al.,Ann. N.Y. Acad. Sci. 569:86-103, 1989; Flexner et al., Vaccine 8:17-21,1990; U.S. Pat. Nos. 4,603,112, 4,769,330, and 5,017,487; WO 89/01973;U.S. Pat. No. 4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805;Berkner, iotechniques 6:616-627, 1988; Rosenfeld et al., Science252:431-434, 1991; Kolls et al., PNAS 91:215-219, 1994; Kass-Eisler etal., PNAS 90:11498-11502, 1993; Guzman et al., Circulation 88:2838-2848,1993; and Guzman et al., Cir. Res. 73:1202-1207, 1993. Techniques forincorporating DNA into such expression systems are well known to thoseof ordinary skill in the art. The DNA may also be “naked,” as described,for example, in published PCT application WO 90/11092, and Ulmer et al.,Science 259:1745-1749 (1993), reviewed by Cohen, Science 259:1691-1692(1993).

Routes and frequency of administration, as well as dosage, will varyfrom individual to individual and may parallel those currently beingused in immunotherapy of other diseases. In general, the pharmaceuticalcompositions and vaccines may be administered by injection (e.g.,intracutaneous, intramuscular, intravenous or subcutaneous),intranasally (e.g., by aspiration) or orally. Between 1 and 10 doses maybe administered over a 3-24 week period. Preferably, 4 doses areadministered, at an interval of 3 months, and booster administrationsmay be given periodically thereafter. Alternate protocols may beappropriate for individual patients. A suitable dose is an amount ofpolypeptide or DNA that is effective to raise an immune response(cellular and/or humoral) against tumor cells, e.g., kidney tumor cells,in a treated patient. A suitable immune response is at least 10-50%above the basal (i.e. untreated) level. In general, the amount ofpolypeptide present in a dose (or produced in situ by the DNA in a dose)ranges from about 1 pg to about 100 mg per kg of host, typically fromabout 10 pg to about 1 mg, and preferably from about 100 pg to about 1μg. Suitable dose sizes will vary with the size of the patient, but willtypically range from about 0.01 mL to about 5 ml.

IMP3 or an immunogenic polypeptide or immunogenic homolog thereof can beused in cell based immunotherapies, e.g., stimulation of dendritic cellswith IMP3 or fusion with IMP3 expressing cells. An “immunogenic homolog”refers to a protein that is at least about 80%, 85%, 90%, 95%, 98% or99% identical to a wildtype IMP3 protein or a fragment thereof. Themodified dendritic cells, once injected into the patient, are a cellularvaccine, where the dendritic cells activate an immune response againstthe IMP3 expressing cancer.

While any suitable carrier known to those of ordinary skill in the artmay be employed in the pharmaceutical compositions of this invention,the type of carrier will vary depending on the mode of administration.For parenteral administration, such as subcutaneous injection, thecarrier preferably comprises water, saline, alcohol, a fat, a wax and/ora buffer. For oral administration, any of the above carriers or a solidcarrier, such as mannitol, lactose, starch, magnesium stearate, sodiumsaccharine, talcum, cellulose, glucose, sucrose, and/or magnesiumcarbonate, may be employed. Biodegradable microspheres (e.g., polylepticgalactide) may also be employed as carriers for the pharmaceuticalcompositions of this invention. Suitable biodegradable microspheres aredisclosed, for example, in U.S. Pat. Nos. 4,897,268 and 5,075,109.

Any of a variety of non-specific immune response enhancers may beemployed in the vaccines of this invention. For example, an adjuvant maybe included. Most adjuvants contain a substance designed to protect theantigen from rapid catabolism, such as aluminum hydroxide or mineraloil, and a nonspecific stimulator of immune response, such as lipid A,Bordella pertussis or Mycobacterium tuberculosis. Such adjuvants arecommercially available as, for example. Freund's Incomplete Adjuvant andComplete Adjuvant (Difco Laboratories. Detroit, Mich.) and MerckAdjuvant 65 (Merck and Company, Inc., Rahway, N.J.).

All publications, patents, patent applications, and GenBank Accessionnumbers mentioned herein are hereby incorporated by reference to theextent necessary to support that for which they have been cited herein.In case of conflict, the present application, including any definitionsherein, will control. The present invention is further illustrated bythe following examples which should not be construed as limiting in anyway. The present invention is further illustrated by the followingexamples which should not be construed as limiting in any way.

EXAMPLES Example 1 The RNA-Binding Protein IMP3: a Novel Biomarker toPredict Metastasis and Prognosis of Renal Cell Carcinomas Summary

Background Distant metastases of renal cell carcinoma (RCC) remain theprimary cause of death in patients with this disease and the metastaticpotential of localized RCC is often unpredictable. In this study, weinvestigated whether IMP3, an oncofetal RNA-binding protein, can serveas a biomarker to predict metastasis and prognosis of RCC.Methods A total of 501 primary and metastatic RCCs were studied. The 371patients with localized primary RCCs were further evaluated for survivalanalysis. The expression of IMP3 in RCC tissues was evaluated byimmunohistochemistry and selected cases were also assessed for mRNA andprotein expression of IMP3 by quantitative real-time polymerase chainreaction and Western blot analysis.Findings The expression of IMP3 was significantly increased not only inthe metastatic RCCs but most importantly also in a subset of primaryRCCs that were much more likely to subsequently develop metastases.Kaplan-Meier plots and log-rank tests showed that patients without IMP3expression in their primary localized RCCs had significant longermetastasis-free survival and overall survival than patients with IMP3expression (P<0.0001). In patients whose localized RCCs were positivefor IMP3 versus those with IMP3 negative RCCs, the 5-yearmetastasis-free survival were 44% vs. 98% [hazards ratio=17.18 (95%confidence interval: 7.82-37.78), stage I], 41% vs. 94% [10.14(3.46-29.68), stage II] and 16% vs. 62% [4.04 (2.23-7.31), stage III],and the 5-year overall survival rates were 32% vs. 89% [6.44(3.63-11.42), stage I], 41% vs. 88% [6.93 (2.63-18.27), stage II] and14% vs. 58% [3.46 (1.98-6.05), stage III] respectively. Multivariate Coxproportional hazards regression analysis showed that the hazard ratio ofIMP3 status in primary RCCs were 5.84 (metastasis-free survival,P<0.0001) and 4.01 (overall survival, P<0.0001) respectively, which weremuch higher than the hazard ratios associated with the other independentrisk factors.Interpretation IMP3 is an excellent independent prognostic marker thatcan be used at the time of initial diagnosis of RCC to identify a groupof patients with a high potential to develop metastasis and who mightbenefit from early systemic therapy.

Introduction

Renal cell carcinoma is the most common type of kidney cancer andaccounts for about 85 percent of malignant kidney tumors^(1,2). Theincidence of renal cell carcinoma has been rising steadily³. It isestimated that there will be about 36,160 new cases of kidney cancer inthe United States in the year 2005, and about 12,660 people will diefrom this disease⁴.

Surgical resection of primary renal cell carcinoma can be a curativetreatment when the disease is localized. However, distant metastasisremains the primary cause of therapeutic failure and cancer death^(1,2).Patients with metastatic disease are typically treated with systemictherapy, which is associated with substantial toxicity^(1,2). Therefore,unless the patient presents with metastatic disease, clinicalobservation is the standard of care following nephrectomy. Currently,the methods to determine prognosis and select patients for postoperativeadjuvant therapy rely mainly on pathological and clinical staging⁵⁻⁸.However, as there are remarkable differences in the biological behaviorof renal cell carcinomas classified in the same stage, it is verydifficult to predict which localized tumor will eventuate in distantmetastasis. Approximately twenty percent of patients with localizedtumors develop metastasis and the median survival for patients withmetastatic disease is approximately 13 months^(2,9,10). Therefore, thereis a great need for biomarkers that can accurately distinguish localizedtumors with a high probability of metastasis from those that will remainindolent. Using such biomarkers, one can predict the patient's prognosisand can effectively target the individuals who would most likely benefitfrom adjuvant therapy. Recently, molecular biomarkers are an area ofinterest for studying renal cell carcinoma. Various protein markers andgene expression profiles based on DNA microarray analysis havedemonstrated potential in predicting disease outcome in renal cellcarcinoma^(11,12).

IMP3 is a member of the insulin-like growth factor II (IGF-II) mRNAbinding protein (IMP) family that consists of IMP1, IMP2 and IMP3¹³. IMPfamily members play an important role in RNA trafficking andstabilization, cell growth, and cell migration during the early stagesof embryogenesis¹⁴. The IMP3 gene is located on chromosome 7p11.2±11cM¹⁵and is identical to the KOC (KH domain containing protein overexpressedin cancer) protein that was originally cloned from a pancreatic tumorcDNA screen¹⁶. IMP3 is expressed in developing epithelium, muscle andplacenta during early stages of human and mouse embryogenesis, but it isexpressed at low or undetectable levels in adult tissues^(13,14). Theexpression of IMP3/KOC is also found in malignant tumors includingpancreas, lung, stomach, and colon cancers, and soft tissue sarcomas butit is not detected in adjacent benign tissues^(13,16,18). Moreover, arecent study has demonstrated that IMP3 promotes human leukemia cellproliferation¹⁹. These findings indicate that IMP3 is an oncofetalprotein that may have a critical role in the regulation of cellproliferation. However, the expression of IMP3 in renal cell carcinomasand the relationship between IMP3 and tumor metastasis are unknown. Inthis study, we investigated whether IMP3 could serve as an independentbiomarker to predict metastasis and prognosis in patients with renalcell carcinoma.

Methods Patients and Tumor Specimens:

Formalin-fixed, paraffin-embedded samples from 406 patients with primaryrenal cell carcinomas, who underwent radical or partial nephrectomy,were obtained from the archival files at the University of MassachusettsMedical Center (UMMC, n=159), the Massachusetts General Hospital (MGH,n=152) and the City of Hope National Medical Center (CHNMC, n=95). Thedata from these sources represented all patients for whom archivaltissues and adequate clinical follow-up information were readilyavailable. All cases were collected between January of 1989 and December2003 and the diagnoses were confirmed by at least two pathologists.Staging was based on pathological findings following the American JointCommittee on Cancer (AJCC) staging manual, sixth edition, 2002. Twohundred sixteen patients (pT1a or b) were stage I, 64 patients (pT2)were stage II, 98 patients (pT3a, n=62; pT3b, n=29; pT3, N1, n=7) werestage III and 28 patients (pT2, N2 or M1, n=5; pT3, N2 or M1, n=12; pT4,N2 or M1, n=7; pT4, n=4) were stage IV. Follow-up for this retrospectivestudy was carried out by researchers (ZJ, PGC, and CLW) reviewing thepatient clinical records. Metastasis was found in 119 of 406 (29%; UMMC:27%; MGH: 29%; CHNMC: 34%) patients with primary RCCs during nephrectomy(N=30) or after surgery (N=89). One hundred fifty nine patients out of406 patients (39%; UMMC: 42%; MGH: 35%; CHNMC:42%) with primary RCCexpired. An additional 95 metastatic renal cell carcinomas (26 of themetastatic RCCs were from the same patients with primary tumors and theothers were from the biopsy or resection of metastatic tumors only),which were obtained from lung (n=22), lymph nodes (n=10),gastrointestinal organs including liver, intestines, pancreas, andgallbladder (n=7), bone (n=23), brain (n=8), adrenal, thyroid and ovary(n=10), head and neck area (n=2), soft tissues (n=6), diaphragm, pleura,retroperitoneum and omentum (n=7) at the three institutions, were alsoexamined by immunohistochemistry (IHC) and compared to the primary RCCs.The Institutional Review Board at each institution approved this study.

Immunohistochemical Analysis

Immunohistochemical studies were performed on 5 μm sections offormalin-fixed, paraffin-embedded tissue from nephrectomy specimens byusing an avidin-biotinylated peroxidase complex system as a previouslypublished protocol¹⁸ on the DAKO Autostainer (DAKO Corporation,Carpinteria, Calif.). Sections of pancreatic carcinoma with knownpositivity of IMP3 were used as positive controls for the L523S mousemonoclonal antibody (MAb) specific for IMP3/KOC (Corixa Corporation,Seattle, Wash.) staining Negative controls were performed by replacingthe primary antibody with nonimmune IgG. Positive staining of IMP3 wasdefined as dark brown cytoplasm (FIGS. 1A and B, IMP3 positive), whilenegative staining of IMP3 was defined as no staining at all (FIG. 1C,IMP3 negative). The status of IMP3 was assessed by a genitourinarypathologist (Z J) without knowledge of the clinical and pathologicalfeatures of the cases or the clinical outcome. To assess thereproducibility of the immunohistochemical test for IMP3 expression, 50cases were randomly chosen for independent analysis in terms of positiveor negative staining by three other pathologists (C W, P C, and C L).There was complete concurrence of the results by all pathologists. Eachpositive case was also further evaluated for the percentage of the cellsthat stained positively and was scored as focal: ≦30%, or diffuse: >30%.

Quantitative Analysis of Immunostaining

A total of 270 different areas (15 different areas per case) from 9 RCCIMP3 positive cases and 9 RCC IMP3 negative cases were quantitativelyanalyzed by a pathologist (ZJ) using a computerized image analyzer(Automated Cellular Imaging System, ACIS, ChromaVision Medical SystemInc., San Juan Capistrano, Calif.) to evaluate the IHC results. WithACIS, positive staining is calculated by applying two thresholds withone recognizing blue background (hematoxylin stained) cells and anotherrecognizing brown positive cells. The integrated optical density (IOD)is that the sum of brown pixels times brown intensity of those pixels.The ACIS values were calculated as IOD was divided by the sum of theblue area and the brown area.

Western Blotting Analysis of IMP3 Expression:

Primary RCC frozen tissues and a metastatic renal cell cancer cell line(ATCC Global Bioresource Center, Manassas, Va., ATCC® Number: HTB-46)were homogenized in 3 volumes of lysis buffer. Immunodetection wasperformed with IMP3 MAb (L523S) at a 1 ug/ml dilution using the enhancedchemiluminescence system (PerkinElmer Life Sciences, Boston, Mass.). Themembrane was stripped and re-blotted with anti-actin (A-2066) polyclonalantibody from Sigma (St. Louis, Mo.). Intensity of the signal wasquantified by densitometry software (NIH Image 1.61) and relativeexpression levels of IMP3 were normalized by amount of the actin in eachlane.

Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR)

IMP3 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH, as an internalreference) mRNA levels in RCC tissues were quantified by qRT-PCR. Frozentissues were cut into 5 micron sections and total RNAs were extracted byQiagen RNeasy Mini Kit (Qiagen, Inc., Valencia, Calif.). Two-stepqRT-PCR was performed with the ABI TaqMan PCR reagent kit (ABI Inc,Foster City, Calif.), and IMP3 primers and GAPDH primers, and the probesfor both genes on ABI Prism 7700 system. The primers were used asfollow: IMP3 forward primer, 5′-GCT AAA GTG AGG ATG GTG ATT ATC ACT-3′(SEQ ID NO: 3); IMP3 reverse primer, 5′-ACT AAC AAA GTT TTC TTC TTT AATTTT TCC AT-3′ (SEQ ID NO: 4); IMP3 probe, 5′ FAM-ACC AGA GGC TCA GTT CAAGGC TCA GGG AA-TAMRA 3′ (SEQ ID NO: 5); GAPDH forward primer,5′-GAAGGTGAAGGTCGGAGTC-3′ (SEQ ID NO: 6); GAPDH reverse primer,5′-GAAGATGGTGATGGGATTTC-3′ (SEQ ID NO: 7); GAPDH probe, 5′FAM-CAAGCTTCCCGTTCTCAGCC-TAMRA 3′ (SEQ ID NO: 8). The expression of IMP3mRNA was normalized with GAPDH mRNA expression measured in the same RNAextraction and calculated as the numbers of IMP3/GAPDH ratio.

Statistical Analysis:

Overall survival was measured from the date of nephrectomy to the dateof death or was censored as of the date of the last follow-up visit forsurvivors. Metastasis-free survival was measured from the date ofsurgery to the date of first clinical evidence of metastasis, and wascensored at the date of death or the date of the last follow-up visitfor survivors. The median follow-up was 63 months (range=1-174 months).Age, sex, size of the tumor, tumor stage, grade and histological type,and IMP3 status were collected as baseline variables. The distributionof each baseline variable was compared for IMP3-positive andIMP3-negative subgroups with the Wilcoxon rank sum test for continuousvariables and the Fisher's exact test for categorical variables.Thirty-one (stage III: N=7 and Stage IV, N=24) of 406 patients withmetastatic disease found during nephrectomy were excluded from theoverall and metastasis-free survival study, as the aim of this study wasto evaluate the risk of metastases after surgery in patients initiallypresenting with localized disease. By AJCC TNM staging criteria, most ofthe stage IV patients (24 of 28, 86%) in this study were found withmetastasis (M1: n=13; N2: n=10; N2 and M1: n=1) during surgery. Onlyfour patients with stage IV disease were found without metastasis duringnephrectomy and they were excluded from the prognostic analysis, as sucha small number of patients would not be informative for the prognosticanalysis of patients with stage IV RCCs. Therefore, a total of 371patients with stage I, II and III disease and without metastasis duringsurgery were included in our survival analysis. Overall survival andmetastasis-free survival of 371 patients were estimated by theKaplan-Meier method and evaluated with the use of log-rank test forunivariate analysis. The Cox proportional-hazard model was used toassess the simultaneous contribution of the following baselinecovariates of age, sex, size of the tumor, tumor stage, grade andhistological type, and IMP3 status. A two-sided P-value of less than0.05 was considered to indicate the statistical significance.

Institutional funds supported this study and funding source had no rolein making decisions including study design, data collection, analysis,and interpretation, writing of the report, and decision to submit.

Results Expression of IMP3 in All Primary and Metastatic Renal CellCarcinomas

IMP3 protein was observed in the cytoplasm of tumor cells (FIGS. 1A and1B). Expression of IMP3 was found in 62% (59 of 95) of metastatic RCCs,in 50% (60 of 119) of primary RCCs with metastases during and afternephrectomy, and in 4% (11 of 287) metastasis-free primary RCCs (FIG.2). In 71 positive primary RCCs, the IMP3 positivity was detected in≦30% tumor cells (focal) in 38 cases, and >30% of tumor cells (diffuse)in 33 cases. No expression of IMP3 was found in benign kidney tissueadjacent to the tumors. The results of quantitative immunohistochemistryshowed significant differences in IMP3 staining values between positiveand negative cases. The average of the ACIS values was 44.3 in the IMP3positive RCCs and 0.01 in the IMP3 negative RCCs (P=0.0025).

In addition, the reactivity of L523S MAb with IMP3/KOC protein producedby RCCs was determined by Western blot analysis (FIG. 3). L523S MAbreacted with a protein at the expected molecular weight for IMP3(approximately 65 kilodalton). FIG. 3 (upper) showed that IMP3 washighly expressed in the metastatic RCC cell line and three IHC positivecases of primary RCCs with subsequent development of metastasis. Incontrast, IMP3 exhibited no expression in two IHC negative cases ofprimary RCCs without the subsequent development of metastasis.

The over expression of IMP3 mRNA was also detected in primary RCCs. Theresults of qRT-PCR performed to quantitatively assess the expressionlevels of IMP3 mRNA in the primary RCCs, which were subject to Westernblot analysis, are shown in FIG. 3 (lower). The three IHC positiveprimary RCCs with subsequent development of metastasis were found toover express IMP3 mRNA as compared to IHC negative primary RCCs withoutdevelopment of metastasis (FIG. 3, lower). Analysis of the agreementbetween the Western blot test and the real-time PCR analysis of the samesamples showed complete agreement between the tests (data not shown).However, since this analysis was based on only five samples, a largerstudy is needed to show conclusive results.

Characteristics of the Patients

Table 1 provides the relevant clinical characteristics of the 406patients with primary RCCs. Age was not correlated with the positivityfor IMP3 (P=0.28). Male patients were more likely than female patientsto show IMP3 expression in their tumors (P=0.015). The expression ofIMP3 was strongly associated with standard pathologic predictors ofclinical outcome. IMP3 expression was found predominately in largetumors, and tumors with higher grade and stage. Only 10-24% of stage I,II and III RCCs expressed IMP3, whereas 50% of stage IV tumors werepositive for IMP3. Expression of IMP3 was found predominately inhigh-grade (grade 3 and 4) tumors and all grade 1 RCCs were negative forIMP3. The IMP3 positivity rate was slightly increased in conventional(clear cell) type carcinomas (23%) as compared with papillary (11%) andchromophobe (15%) RCCs. Two cases of unclassified RCCs were all positivefor IMP3. IMP3 expression in primary RCCs was associated with asignificant increase in the risk of death. Ninety percent (64 of 71) ofpatients with expression of IMP3 died and 28% (95 of 335) of patientswithout IMP3 expression expired.

TABLE 1 Clinicopathological Characteristics of Renal Cell CarcinomaPatients IMP3+ IMP3− P Characteristic (N = 71) (N = 335) Value Sex:Female 17 (11%) 132 (89%)  0.015 Male 54 (21%) 203 (79%)  Age - yr 61.8± 11.2* 59.5 ± 14.1 0.28 Tumor stage I 22 (10%) 194 (90%)  <0.0001 II 11(17%) 53 (83%) III 24 (24%) 74 (76%) IV 14 (50%) 14 (50%) Tumor Size 8.5± 4.9* 6.1 ± 3.7 <0.0001 Tumor Grade 1 0 (0%)  30 (100%) <0.0001 2 17(9%)  169 (91%)  3 36 (24%) 111 (76%)  4 18 (42%) 25 (58%) Histologicaltypes Clear cell type 58 (23%) 256 (74%)  0.04 Papillary  7 (11%) 56(89%) Chromophobe  4 (15%) 23 (85%) Unclassified  2 (100%) 0 (0%)*Plus-minus values are means ± SD.Expression of IMP3 and Prognosis in Patients with Localized Renal CellCarcinoma During Nephrectomy

A total of 371 patients who did not have metastasis at the time ofsurgery were included in follow-up analysis. The percentage ofmetastasis after surgery was significantly different between the IMP3positive patients and the IMP3 negative patients in their primary RCCs.Eighty percent (43 of 54) of patients with IMP3 positivity in theirprimary RCCs subsequently developed metastasis (median follow-up=38months, range=1-155 months), whereas 13% (41 of 317) of patients withoutexpression of IMP3 in their primary tumors were found to have metastasesafter surgery (median follow-up=70 months, range=1-174 months).

Kaplan-Meier plots and log-rank tests in all patients (n=371) withlocalized disease at the time of surgery and in these 371 patientsseparated into each stage (Stage I, n=216; Stage II, n=64; Stage III,n=91) showed that patients without IMP3 expression in their primary RCCshad significant longer metastasis-free survival and overall survivalthan patients with IMP3 expression. FIG. 4A showed that the 5-yearmetastasis-free survival rate was 89% in IMP3 negative patients versus33% in IMP3 positive patients. The 5-year overall survival rate was 82%in patients without expression of IMP3 versus 27% in patients with IMP3expression (FIG. 4B). In patients with stage I (FIGS. 5A and B), II(FIGS. 5C and D), and III (FIGS. 5E and F) renal cell cancers, thestatus of IMP3 expression was also significantly associated withincreased risk of metastasis and was strongly linked to poor overallsurvival rate. Univariate analysis showed that hazard ratios (HR) ofIMP3 expression were 9.22 (for metastasis-free survival; 95% confidenceinterval, 6.01-14.14; P<0.0001) and 5.66 (for overall survival; 95%confidence interval, 3.93-8.16; P<0.0001) respectively (Table 2). Inpatients whose localized RCCs were positive for IMP3 versus those withIMP3 negative RCCs, the 5-year metastasis-free survival were 44% vs. 98%[hazards ratio=17.18 (95% confidence interval: 7.82-37.78), stage I],41% vs. 94% [10.14 (3.46-29.68), stage II] and 16% vs. 62% [4.04(2.23-7.31), stage III], and the 5-year overall survival rates were 32%vs. 89% [6.44 (3.63-11.42), stage I], 41% vs. 88% [6.93 (2.63-18.27),stage II] and 14% vs. 58% [3.46 (1.98-6.05), stage III] respectively.

TABLE 2 Univariate Cox Proportional Hazard Regression Analysis forMetastasis-free and Overall Survival Metastasis-Free Survival OverallSurvival Hazard Ratio P Hazard Ratio P Variable (95% CI) Value (95% CI)Value IMP3 Status  9.22 (6.01-14.14) <0.0001 5.66 (3.93-8.16) <0.0001 (+vs. −) Age 1.01 (1.00-1.03) 0.167 1.03 (1.02-1.04) <0.0001 Sex (F vs. M)0.77 (0.48-1.21) 0.250 0.94 (0.65-1.34) 0.722 Tumor Size 1.16(1.12-1.21) <0.0001 1.10 (1.06-1.15) <0.0001 Tumor Stage II vs. I 1.85(0.96-3.53) 0.065 1.21 (0.72-2.02) 0.470 III vs. I 6.05 (3.71-9.84)<0.0001 3.39 (2.32-4.96) <0.0001 Tumor Grade 2 vs. 1 4.40 (0.60-32.4)0.146 1.22 (0.52-2.87) 0.646 3 vs. 1 11.37 (1.57-82.6)  0.016 2.59(1.12-6.01) 0.027 4 vs. 1 18.44 (2.44-139.6) 0.005  4.42 (1.78-10.96)0.001 Histological type Papillary vs. Clear 0.48 (0.23-0.99) 0.047 0.66(0.39-1.12) 0.121 Chromophobe vs. Clear 0.90 (0.39-2.08) 0.808 0.75(0.35-1.61) 0.454

The IMP3 positive staining patterns (focal vs. diffuse) in the primaryRCCs did not alter the patients' prognosis. There were no significantdifferences in metastasis-free survival (P=0.732) and overall survival(P=0.728) between patients with focal IMP3 staining and patients withdiffuse IMP3 staining in their primary RCCs. No significant differenceof overall survival is found between IMP3 positive and IMP3 negativepatients with stage IV disease (P=0.14).

Multivariable Analysis

The results of the multivariable analysis, which was stratified by threedifferent centers in this study, for metastasis-free survival andoverall survival in the 371 patients with localized disease at the timeof surgery are presented in Table 3. For these analyses, all factorsshown in table 1 were initially included in the model as potential riskfactors. Multivariable Cox proportional hazards regression analysisshowed that the expression of IMP3 in primary RCCs was a strongindependent predictor of the patients' clinical outcome. The hazardratios were 5.84 (for metastasis-free survival; 95% confidence interval,3.60 to 9.49; P<0.0001) and 4.01 (for overall survival; 95% confidenceinterval, 2.66 to 6.05; P<0.0001) respectively, which were much higherthan the hazard ratios associated with all other independent riskfactors (Table 3). In addition to IMP3 status, age and tumor stage III(compared to stage I) were also observed as significant risk factors foroverall survival, and tumor size and tumor stage III (compared to stageI) were also observed as significant factors for metastasis-freesurvival (Table 3).

TABLE 3 Multivariable Cox Proportional Hazard Regression Analysis forMetastasis-free and Overall Survival Metastasis-Free Survival OverallSurvival Hazard Ratio P Hazard Ratio P Variable (95% CI) Value (95% CI)Value IMP3 Status 5.84 (3.60-9.49) <0.0001 4.01 (2.66-6.05) <0.0001 (+vs. −) Age 1.00 (0.98-1.02) 0.752 1.02 (1.01-1.04) 0.006 Sex 1.08(0.66-1.77) 0.747 1.08 (0.73-1.59) 0.694 Tumor Size 1.11 (1.04-1.18)0.001 1.05 (0.99-1.11) 0.081 Tumor Stage II vs. I 0.73 (0.30-1.77) 0.4840.87 (0.44-1.71) 0.677 III vs. I 3.15 (1.72-5.77) <0.0001 2.08(1.30-3.33) 0.002 Tumor Grade 2 vs. 1 2.02 (0.27-15.37) 0.496 0.89(0.37-2.16) 0.797 3 vs. 1 4.43 (0.59-33.54) 0.149 1.57 (0.64-3.84) 0.3194 vs. 1 3.22 (0.40-25.80) 0.272 1.27 (0.47-3.44) 0.634 Histological typePapillary vs. 0.50 (0.22-1.11) 0.090 0.71 (0.41-1.25) 0.236 ClearChromophobe 1.29 (0.54-3.08) 0.564 0.95 (0.44-2.09) 0.908 vs. Clear

Discussion

Distant metastasis of renal cell carcinomas is the primary cause ofdeath and therapeutic failure^(1,2). Although tumor stage, grade andsubtype provide some prognostic information, the metastatic potential oflocalized RCC is often unpredictable. Since a well-characterizedantibody to IMP3, but not IMP1 or IMP2, was available forimmunohistochemical study, we investigated IMP3 expression in primaryRCC and metastatic RCC as part of our program to develop biomarkers forclinical use. After we found that the expression of IMP3 wassignificantly increased in metastatic RCCs as compared to primary RCCs,we examined the relationship between IMP3 expression and progression inprimary RCCs. Our findings demonstrate that the expression of IMP3 inprimary renal cell carcinomas can predict tumor metastasis and provideimportant prognostic information in patients with localized disease whoundergo nephrectomy. IMP3 displays several features that make it anattractive prognostic marker for renal cell carcinoma. First, theexpression of IMP3 is correlated with other known pathologicalindicators of aggressive RCCs. Our results showed that the expression ofIMP3 was strongly related to higher tumor grade and stage, and largertumor size.

Second, the expression of IMP3 in primary RCCs is independently linkedto poor clinical outcome. Overall survival of patients with expressionof IMP3 was extremely poor as compared to that of patients without IMP3expression in primary localized RCCs and this was independent of tumorstage. Patients with IMP3 expression died at a rate 4 times greater thanpatients without IMP3 expression. Remarkably, the multivariate Coxanalysis showed that the hazard ratios for death in patients withpositive IMP3 in the primary tumor was much higher than the hazardratios associated with any other clinical and pathological predictorsincluding age, sex, and tumor stage, size, grade and subtype.

Third, the expression of IMP3 is an independent predictor of tumormetastasis. A decreased overall survival rate was strongly associatedwith a high metastatic rate in IMP3 positive patients. Out data showedthat the expression of IMP3 was significantly increased not only inmetastastic renal cell carcinomas but most importantly also in patientswith primary renal cell cancers who developed metastatic disease ascompared with renal cell cancers without metastasis. We found that 80%of patients with IMP3 positivity in their localized RCCs developedmetastasis, whereas only 13% of patients without expression of IMP3 intheir primary tumors developed metastases. In patients with stage IIIdisease, almost all of IMP3 positive patients developed metastases afternephrectomy. In the multivariable Cox analysis, patients with IMP3expression in their primary RCCs developed metastasis at a rate, whichis 5.84 times greater than patients without expression of IMP3 adjustingfor other well-known clinical variables.

Fourth, IMP3 immunohistochemical staining is a simple, inexpensive andreliable assay. As localized renal cell cancers are usually treated bypartial or radical nephrectomy, tumor tissue is routinely available forimmunohistochemical staining with the monoclonal L523S antibody. Ourstudy showed that pathologists can readily analyze IMP3immunohistochemistry without inter observer variation to determinepositive and negative staining, which can be easily applied in routineclinical practice in all patients with nephrectomy. A computerized imageanalyzer for quantitative immunohistochemistry (ACIS), which has beenclinically used for evaluation of Her2/neu gene expression, alsoconfirmed the accuracy of the evaluation of the IMP3 immunostainingresults by pathologists. In this study, we mainly focused on evaluationof IMP3 immunostaining by pathologists and used ACIS as a confirmatorytest. A further study is necessary to determine how quantitative imageanalysis of immunostaining results correlates with patient outcome.

Fifth, as patients whose tumors express IMP3 have a high potential todevelop metastasis, IMP3 provides a marker that not only can identify asubgroup of the patients who might benefit from a different follow-upapproach after nephrectomy, but also can be used at initial diagnosiswhich would be the optimal time for considering early systemic therapy.Although the expression of IMP3 was found in multiple malignant tumorsbut not in adjacent benign tissues^(11,12,15,16), and a recent studydemonstrated that IMP3 may have a critical role in the regulation ofcell proliferation¹⁷, little is known of the biological function of IMP3in tumor pathogenesis. Our findings raise the possibility that IMP3, asan oncofetal protein, may play a direct role in the metastasis and/ormore lethal behavior of renal cell carcinoma. Interestingly, Yaniv et alfound that IMP3 in Xenopus laevis ¹³ is required for the migration ofcells forming the roof plate of the neural tube and, subsequently, forneural crest migration²⁰. The findings indicated that IMP3 plays animportant role in promoting cell migration. Further study is required toinvestigate whether IMP3 plays a direct role in the biological behaviorof metastatic RCC.

In summary, IMP3 serves as an excellent independent prognostic markerfor renal cell carcinoma. IMP3 expression status in primary renal cellcancers may identify a subgroup of patients, particularly in patientswith early-stage disease, who have a high potential to developmetastasis after surgery and die from the disease. The findings may havetherapeutic implications in a group of patients who may benefit fromearly systematic therapy after nephrectomy.

REFERENCES

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Example 2 Association of IMP3 Tumor Expression with ClinicopathologicFeatures and Patient Outcome Among Patients with Papillary andChromophobe Renal Cell Carcinoma Introduction

IMP3 is a member of the insulin-like growth factor-II (IGF-II) mRNAbinding protein family. Although IMP3 is expressed within developingepithelia, myocytes, and placenta during human and mouse embryogenesis,its expression is low or undetectable in post-natal tissues andvirtually absent in adult tissues. IMP3 is thought to participate in theprotection and intracellular distribution of IGF-II mRNA and, thus, hasbeen implicated in regulating the production of IGF-II. Interestingly,some reports suggest that renal cell carcinoma (RCC) tumors, especiallyaggressive tumors exhibiting sarcomatoid differentiation, expressincreased IGF-II expression. Moreover, overexpression of IGF-IR, acognate cell-surface receptor for IGF-I and II, has also been observedin RCC tumors and implicated as a feature of aggressive tumor behavior.Jiang et al.¹ systematically studied the expression of IMP3 in a cohortof 371 patients with localized tumors of the clear cell, papillary, orchromophobe RCC subtypes. In this study, Jiang et al.¹ reported thattumor cell IMP3 expression was significantly associated with progressionto distant metastases and death, even after multivariate adjustment forpatient age, sex, tumor size, stage, grade and histologic subtype. Thesefindings were recently independently validated using a cohort of 629consecutively-treated patients with localized clear cell RCC (Hoffmannet al, under review at Cancer Research). The various RCC subtypesincluding papillary RCC and chromophobe RCC have distinct genetic andmorphologic characteristics.²⁻⁵ Papillary and chromophobe RCCs accountsfor approximately 25% of RCCs. Clear cell RCCs has worse cancer specificsurvival compared to papillary and chromophobe RCCs (ref 4). However,there is no large study for IMP3 expression in these various RCCs. Thegoal of the current study is to evaluate the association of IMP3expression with clinicopathologic features and outcome using amulti-institutional cohort of patients with the papillary andchromophobe RCC subtypes.

Materials and Methods Patient Selection

Using the combined resources of the Mayo Clinic, the University ofMassachusetts Medical Center (UMMC), Massachusetts General Hospital(MGH), and City of Hope National Medical Center (CHNMC), we identified334 patients treated with radical nephrectomy or nephron-sparing surgeryfor papillary or chromophobe RCC. The Mayo Clinic patients (N=246) weretreated between 1990 and 1999, while the UMMC (N=39), MGH (N=38), andCHNMC (N=11) patients were treated between 1989 and 2003.¹ There were254 (76.0%) patients with papillary RCC and 80 (24.0%) with chromophobeRCC.

Clinicopathologic Features

The clinicopathologic features studied included age, sex, histologicsubtype classified according to the Union Internationale Contre leCancer, American Joint Committee on Cancer, and Heidelbergguidelines^(2,3), tumor size, primary tumor classification, regionallymph node involvement, distant metastases, the TNM stage groupings, andnuclear grade.

IMP3 Immunohistochemical Staining

Immunohistochemical studies were performed by the Department ofPathology at the UMMC on 5-um sections of formalin-fixed,paraffin-embedded tissue as previously described.¹ Antigen retrieval wascarried out with 0.01 mol/L citrate buffer at pH 6.0, in an 800-Wmicrowave oven for 15 minutes before immunostaining The slides werestained on the DAKO Autostainer (DAKO Corporation, Carpinteria, Calif.)using the EnVision (Dako) staining reagents. The sections were firstblocked for endogenous protein binding and peroxidase activity with anapplication of Dual Endogenous Block (Dako) for 10 minutes, followed bya buffer wash. The sections were then incubated with a mouse monoclonalantibody specific for IMP3 (L523S, Corixa, Seattle, Wash.) at a 2.0μg/ml concentration for 30 minutes, followed again by a buffer wash.Sections were then incubated with the EnVision+Dual Link reagent (apolymer conjugated with goat-anti-mouse-Ig, and horseradish peroxidase)for 30 minutes. The sections were then washed, and treated withdiaminobenzidine (DAB) and hydrogen peroxide, which reacted to visualizethe end product. A toning solution (DAB Enhancer, Dako) was used toenrich the final color. The sections were counterstained withhematoxylin, dehydrated, and coverslipped with permanent media. Sectionsof urothelial carcinoma with known positivity of IMP3 were used aspositive controls for the L523S mouse monoclonal antibody (MAb) specificfor IMP3/KOC (Corixa Corporation, Seattle, Wash.) staining Negativecontrol sections were stained by replacing the primary antibody withnon-immune mouse IgG (Vector, Burlingame Calif.) at 2.0 ug/ml.

IMP3 Quantitation

IMP3 tumor expression was recorded as negative or positive after visualassessment by a genitourinary pathologist (ZJ) without knowledge ofpatient outcome.

Statistical Methods

Associations of IMP3 expression with clinicopathologic features wereevaluated using Wilcoxon rank sum, chi-square, and Fisher's exact tests.Kaplan-Meier curves were used to visualize the associations of IMP3expression with outcome. The magnitude of these associations wereevaluated using Cox proportional hazards regression models andsummarized with risk ratios and 95% confidence intervals (CI).Statistical analyses were performed using the SAS software package (SASInstitute; Cary, N.C.). All tests were two-sided and p-values<0.05 wereconsidered statistically significant.

Results

There were 294 (88.0%) papillary or chromophobe RCC tumors with negativeIMP3 expression and 40 (12.0%) with positive IMP3 expression.Comparisons of clinicopathologic features by IMP3 expression aresummarized in Table 4. Positive IMP3 tumor expression was significantlyassociated with later tumor stage and higher tumor grade. For example,70% of the IMP3-positive tumors were high grade (i.e., grade 3 or 4)compared with only 37% of the IMP3-negative tumors (p<0.001).

TABLE 4 Comparison of Clinicopathologic Features by IMP3 TumorExpression for 334 Patients with Papillary and Chromophobe RCC TumorIMP3 Expression Negative Positive Feature N = 294 N = 40 P-value Median(Range) Age at Surgery (Years)  65 (21-89)  63 (44-80) 0.883 Tumor Size(cm)   4.1 (0.3-15.0)   5.5 (0.7-25.0) 0.090 N (%) Sex Female 68 (23.1) 9 (22.5) 0.929 Male 226 (76.9)  31 (77.5) RCC Histologic SubtypePapillary 228 (77.6)  26 (65.0) 0.081 Chromophobe 66 (22.5) 14 (35.0)Primary Tumor Classification pT1 213 (72.5)  21 (52.5) 0.008 pT2 49(16.7)  7 (17.5) pT3 31 (10.5) 12 (30.0) pT4 1 (0.3) 0 Regional LymphNode Involvement pNX and pN0 289 (98.3)  35 (87.5) 0.003 pN1 and pN2 5(1.7)  5 (12.5) Distant Metastases at Presentation pM0 289 (98.3)  37(92.5) 0.058 pM1 5 (1.7) 3 (7.5) 2002 TNM Stage Groupings I 211 (71.8) 21 (52.5) 0.002 II 48 (16.3)  6 (15.0) III 28 (9.5)   7 (17.5) IV 7(2.4)  6 (15.0) Nuclear Grade 1 9 (3.1) 0 <0.001 2 176 (59.9)  12 (30.0)3 103 (35.0)  19 (47.5) 4 6 (2.0)  9 (22.5)

There were 17 patients with papillary or chromophobe RCC who hadextrarenal disease at nephrectomy, including 9 with regional lymph nodeinvolvement, 7 with distant metastases, and 1 with both. As such,associations of IMP3 expression with patient outcome were evaluatedusing the 317 patients with localized disease at nephrectomy (i.e.,pNX/pN0; pM0; stage groups I, II, or III). In this subset, there were284 (89.6%) papillary or chromophobe RCC tumors with negative IMP3expression and 33 (10.4%) with positive IMP3 expression.

Twenty-eight of the 317 patients with localized disease progressed todistant metastases at a median of 3.1 years following nephrectomy (range0-10).

Patients with localized IMP3-positive tumors were over 10 times morelikely to progress to distant metastases compared with patients withlocalized IMP3-negative tumors (risk ratio 11.38; 95% CI 5.40-23.96;p<0.001; Table 5). In fact, 15 (45.5%) of the 33 patients withIMP3-positive tumors progressed compared with only 13 (4.6%) of the 284patients with IMP3-negative tumors. Metastases-free survival rates (SE,number still at risk) at 5 and 10 years following nephrectomy were 63.9%(8.8%, 17) and 48.6% (9.5%, 12), respectively, for patients withIMP3-positive tumors compared with 97.7% (0.9%, 223) and 93.4% (1.9%,86), respectively, for patients with IMP3-negative tumors (FIG. 6). Inmultivariate analysis adjusting for the TNM stage groupings and nucleargrade, patients with IMP3-positive tumors were still over 10 times morelikely to progress compared with patients with IMP3-negative tumors(risk ratio 13.45; 95% CI 6.00-30.14; p<0.001; Table 5). IMP3 expressionwas univariately significantly associated with progression to distantmetastases among patients with papillary RCC (risk ratio 9.14; 95% CI3.39-24.64; p<0.001) as well as among patients with chromophobe RCC(risk ratio 11.91; 95% CI 3.58-39.61; p<0.001), although there were toofew patients who progressed in these subsets to evaluate theseassociations in a multivariate setting.

TABLE 5 Associations of IMP3 Tumor Expression with Outcome for 317Patients with Localized Papillary and Chromophobe RCC Overall SurvivalMetastases-free Survival Risk Risk Ratio (95% CI) P-value Ratio (95% CI)P-value Univariate IMP3 Expression Negative  1.0 (reference)  1.0(reference) Positive 11.38 (5.40-23.96) <0.001 1.91 (1.13-3.22) 0.016Multivariate TNM Stage Groupings I  1.0 (reference)  1.0 (reference) II 4.38 (1.69-11.36) 0.002 0.97 (0.55-1.68) 0.900 III 10.94 (4.18-28.68)<0.001 2.28 (1.29-4.04) 0.005 Nuclear Grade 1 and 2  1.0 (reference) 1.0 (reference) 3 and 4  5.30 (1.94-14.49) 0.001 1.38 (0.93-2.06) 0.112IMP3 Expression Negative  1.0 (reference)  1.0 (reference) Positive13.45 (6.00-30.14) <0.001 1.95 (1.15-3.31) 0.013

At last follow-up 103 patients had died at a median of 4.5 yearsfollowing nephrectomy (range 0-16). Among the 214 patients who werestill alive at last follow-up, the median duration of follow-up was 8.8years (range 0-16). Overall survival rates (SE, number still at risk) at5 and 10 years following nephrectomy were 82.2% (2.2%, 240) and 65.4%(3.1%, 98), respectively. There was not a statistically significantdifference in overall survival between patients with localized papillaryand chromophobe RCC (p=0.997; log-rank test).

Univariately, patients with localized IMP3-positive tumors were nearlytwice as likely to die compared with patients with localizedIMP3-negative tumors (risk ratio 1.91; 95% CI 1.13-3.22; p=0.016; Table5). Seventeen (51.5%) of the 33 patients with IMP3-positive tumors diedcompared with 86 (30.3%) of the 284 patients with IMP3-negative tumors.Overall survival rates (SE, number still at risk) at 5 and 10 yearsfollowing nephrectomy were 57.9% (9.0%, 17) and 47.1% (9.2%, 12),respectively, for patients with IMP3-positive tumors compared with 85.0%(2.2%, 223) and 67.4% (3.3%, 86), respectively, for patients withIMP3-negative tumors (FIG. 7). In multivariate analysis adjusting forthe TNM stage groupings and nuclear grade, patients with IMP3-positivetumors were still nearly twice as likely to die compared with patientswith IMP3-negative tumors (risk ratio 1.95; 95% CI 1.15-3.31; p=0.013;Table 5).

REFERENCES

-   1. Jiang Z, Chu P G, Woda B A, et al. Analysis of RNA-binding    protein IMP3 to predict metastasis and prognosis or renal-cell    carcinoma: a retrospective study. Lancet Oncology 2006; 7:556-564.-   2. Storkel S, Eble J N, Adlakha K, et al. Classification of renal    cell carcinoma: Workgroup No. 1. Union Internationale Contre le    Cancer (UICC) and the American Joint Committee on Cancer (AJCC).    Cancer 1997; 80:987-989.-   3. Kovacs G, Akhtar M, Beckwith B J, et al. The Heidelberg    classification of renal cell tumors. Journal of Pathology 1997;    183:131-133.-   4. Cheville J C, Lohse C M, Zincke H, et al. Comparisons of outcome    and prognostic features among histologic subtypes of renal cell    carcinoma. American Journal of Surgical Pathology 2003; 27:612-624.-   5. Lohse C M and Cheville J C. A review of prognostic pathologic    features and algorithms for patients treated surgically for renal    cell carcinoma. Clinics in Laboratory Medicine 2005; 25:433-464.

Example 3 Combination of Expression of IMP3 and Tumor Staging: a NewSystem to Predict Metastasis for Patients with Localized Renal CellCarcinomas Abstract

Purpose: We investigate whether the levels of expression of a newprognostic biomarker (IMP3) combined with tumor staging can serve as anew system to predict metastasis of localized renal cell carcinoma.Design: The 369 patients with localized RCCs from three institutionswere investigated by use of survival analysis. The expression of IMP3was evaluated by immunohistochemistry and a computerized image analyzer(Automated Cellular Imaging System). Combining quantitative IMP3 resultswith tumor staging (QITS system) generated four distinct groups ofpatients.Result: Four groups of patients in QITS system showed significantdifferences for their metastasis-free (P<0.0001) and overall survivals(P<0.0001). Almost all patients of group IV with localized RCCsdeveloped metastasis (sub clinical metastasis) and died afternephrectomy. The 5 and 10 year metastasis-free survival rates for theQITS groups were as follows for groups: I, 97% and 91%, II, 62% and 55%,III, 46% and 19%, and V, 17% and 4%, respectively. The 5 and 10 yearoverall survival rates for the QITS groups were as follows for groups:I, 89% and 72%, II, 58% and 41%, III, 38% and 17%, and V, 14% and 4%,respectively.Conclusion: Our findings suggest that combining quantitative IMP3expression and tumor staging provide a unique, simple and accuratesystem to predict tumor metastasis. This system will provide importantprognostic information for patients with localized RCCs and will helpphysicians to select high risk patients to start systematic therapyright after nephrectomy.

Introduction

Renal cell carcinoma accounts for about 85% of all malignant kidneytumors in the United States, making it the most common type of kidneycancer^(1,2). The incidence of this type of carcinoma has been risingsteadily³. It was expected that about 38,890 new cases of kidney cancerwould be diagnosed in the U.S. in 2006 with approximately 12,840mortalities⁴.

Currently surgical resection of tumor (nephrectomy) is the standard ofcare for almost all patients with renal cell carcinoma^(1,2,5). Afternephrectomy, patients with metastatic disease typically receive systemictreatment (e.g. immunotherapy), which is associated with significanttoxic side effects^(1,2,5). In order to avoid the multiple toxicitiesassociated with treatment, watchful waiting is the standard of carefollowing nephrectomy unless the patient presents with clearlymetastatic disease^(1,2,5). Recently, two new drugs, Nexavar®(sorafenib) and Sutent® (sunitinib), the multi kinase receptorinhibitors, which can block the signal cascade of the vascularendothelial growth factor (VEGF) 2, 3 and R1, as well asplatelet-derived growth factor (PDGF) that are critical to angiogenesis,have been used for treatment of patients with metastatic renal cellcarcinoma⁶⁻⁹. However, these new drugs were only evaluated in patientswith clinically metastaticRCC⁶⁻⁹.

The metastastic potential of localized tumors is often unpredictable.Currently, evaluation of patients for post-nephrectomy adjuvant therapyrelies almost entirely on clinical and pathological staging¹⁰⁻¹³. Renalcell cancers that are typically classified at the same stage exhibitmarkedly different biological behavior¹⁰⁻¹³. Consequently, 30% ofpatients with localized tumor during surgery will subsequently recur andmetastasize and the survival rates of these are typically less than10%^(14,15). Therefore, there is still a great need for biomarkers topredict patients' metastasis, particularly for early stages (stage I, IIand III) of RCC. A reliable biomarker that can at the time of initialdiagnosis of localized disease distinguish between tumors which willremain indolent following nephrectomy from those with early stage oftumor and a high probability for metastasis will allow clinicians toearly target those individual patients who are most likely to benefitfrom adjuvant therapy, particularly from sorafenib and sunitinib therapywhile sparing patients who are less likely to suffer metastasis from theside effects of systemic treatment.

IMP3 is a member of a family of conserved RNA-binding proteins thatconsists of IMP1, IMP2 and IMP3¹⁶. These IMP of proteins all contain twoRNA recognition motifs and 4 K-homology domains that allow them to bindRNAs strongly and specifically, however only a few specific RNA targets,such as insulin-like growth factor II (IGF-II) have thus far beenidentified^(17,18). IMP3 has also been called KOC (K-homology domainprotein over expressed in cancer) and L523S^(17,19). IMP3 is expressedin developing epithelium, muscle and placenta during early stages ofhuman and mouse embryogenesis^(16,18). In contrast, it is expressed atlow or undetectable levels in adult tissues. Certain cancers alsoexpress IMP3^(17,19,20). In fact, it was identified in screens for genesover expressed in pancreatic and lung cancers^(17,19,20). It has beenreported to be also expressed in carcinomas of the stomach and colon andsoft tissue sarcomas¹⁶. Thus, IMP3 is an oncofetal antigen.

Recently, we have discovered that IMP3 is expressed in a subset of renalcell carcinomas and its expression predicts remarkably well the RCCsthat progress to metastasis²¹. In previous study, we have demonstratedIMP3 status and tumor stage are the two most important risk factors forpredicting metastasis of localized RCC. In this study, we used acomputerized image analyzer [Automated Cellular Imaging System (ACIS)]to quantitative analysis of the immunohistochemistry IMP3 in localizedRCCs and determined whether tumors with higher levels of IMP3 mayprogress more rapidly than those with lower levels of this molecule andwhether combining the levels of IMP3 expression of IMP3 and tumor stagecan serve as a new system to more accurately predict metastasis oflocalized renal cell carcinoma.

Materials and Methods

Patients and Tumor Specimens: Formalin-fixed, paraffin-embedded samplesfrom 369 patients with localized primary renal cell carcinomas, whounderwent radical or partial nephrectomy, were obtained from thearchival files at the University of Massachusetts Medical Center (UMMC,n=144), the Massachusetts General Hospital (MGH, n=147) and the City ofHope National Medical Center (CHNMC, n=78). The data from these sourcesrepresented all patients for whom archival tissues and adequate clinicalfollow-up information were readily available. All cases were collectedbetween January of 1989 and December 2003 and the diagnoses wereconfirmed by at least two pathologists. Staging was based onpathological findings following the American Joint Committee on Cancer(AJCC) staging manual, sixth edition, 2002. Two hundred fifteen patients(pT1a or b) were stage I, 63 patients (pT2) were stage II, 91 patients(pT3a, N0, n=62; pT3b, N0, n=29) were stage III. Follow-up for thisretrospective study was carried out by reviewing the patient clinicalrecords. Overall survival was measured from the date of nephrectomy tothe date of death or was censored as of the date of the last follow-upvisit for survivors. Metastasis-free survival was measured from the dateof surgery to the date of first clinical evidence of metastasis, and wascensored at the date of death or the date of the last follow-up visitfor survivors. The median follow-up was 63 months (range=1-174 months).The Institutional Review Board at each institution approved this study.Immunohistochemical Analysis: Immunohistochemical studies were performedon 5 μm sections of formalin-fixed, paraffin-embedded tissue fromnephrectomy specimens by using an avidin-biotinylated peroxidase complexsystem as a previously published protocol²⁰ on the DAKO Autostainer(DAKO Corporation, Carpinteria, Calif.). Sections of pancreaticcarcinoma with known positivity of IMP3 were used as positive controlsfor the L523S mouse monoclonal antibody (MAb) specific for IMP3/KOC(Corixa Corporation, Seattle, Wash.) staining Negative controls wereperformed by replacing the primary antibody with nonimmune IgG.Quantitative Analysis of Immunostaining: A total of 1,845 tumor areas (5different areas/case) from all RCC tissues were quantitatively analyzedby a computerized image analyzer (Automated Cellular Imaging System,ACIS, ChromaVision Medical System Inc., San Juan Capistrano, Calif.) toevaluate the IHC results. With ACIS, positive staining is calculated byapplying two thresholds with one recognizing blue background(hematoxylin stained) cells and another recognizing brown positivecells. The integrated optical density (IOD) is that the sum of brownpixels times brown intensity of those pixels. The ACIS values werecalculated as IOD was divided by the sum of the blue area and the brownarea. IMP3 expression in RCCs was considered to be negative (averageACIS value/case: <1) and positive (average ACIS value/case: ≧1; lowlevels of expression: ACIS values=1 to 10, and high levels ofexpression: ACIS values>10).Statistical Analysis Age, sex, size of the tumor, tumor stage and grade,and IMP3 status were collected as baseline variables. The distributionof each baseline variable was compared for IMP3-positive andIMP3-negative subgroups with the Wilcoxon rank sum test for continuousvariables and the Fisher's exact test for categorical variables. Overallsurvival and metastasis-free survival of 369 patients were estimated bythe Kaplan-Meier method and evaluated with the use of log-rank test forunivariate analysis. The Cox proportional-hazard model was used toassess the simultaneous contribution of the following baselinecovariates of age, sex, size of the tumor, tumor stage and grade, andIMP3 status. A two-sided P-value of less than 0.05 was considered toindicate the statistical significance.Based on a Cox proportional-hazard model, IMP3 status and tumor stagewere the two most important independent risk factors for predictingmetastasis of localized RCC, the levels (low versus high) of IMP3expression from ACIS analysis and tumor stage were divided into fivesubgroups each of which had a significantly increasing risk ofmetastasis and death over the previous one.

Results

Patients based on IMP3 status of their RCCs including negative, low andhigh expression, and tumor stage were classified into four groups(Tables 6 and 7). This QITS system showed significant differences fortheir metastasis-free (P<0.0001) and overall survivals (P<0.0001). FIG.9 showed significant stratification of high risk patients compared toTNM staging alone (FIG. 8). Almost all patients of group IV withlocalized RCCs developed metastasis (sub clinical metastasis) and diedafter nephrectomy (FIG. 9). The 5 and 10 year metastasis-free survivalrates for the QITS groups were as follows for groups: I, 97% and 91%,II, 62% and 55%, III, 46% and 19%, and V, 17% and 4%, respectively(Table 7). The 5 and 10 year overall survival rates for the QITS groupswere as follows for groups: I, 89% and 72%, II, 58% and 41%, III, 38%and 17%, and V, 14% and 4%, respectively (Table 8).

TABLE 6 Quantitative IMP3 Status of RCC Combined with Tumor Stage (QITS)System QITS Groups IMP3 Status Tumor Stage I Negative Stage 1 and 2 IINegative Stage 3 III Low Expression Stage 1 IV Low Expression Stage 2and 3 High Expression Stage 1, 2 and 3

TABLE 7 QITS and TNM Systems with 5- and 10 Year Metastasis-freeSurvivals QITS Groups I II III VI 5-Year Metastasis 97% 63% 46% 17% freeSurvival 10-Year Metastasis 91% 55% 19% 4% free Survival TNM Stage I IIIII 5-Year Metastasis 92% 85% 51% free Survival 10-Year Metastasis 84%69% 40% free Survival

TABLE 8 QITS and TNM Systems with 5- and 10 Year Overall Survivals QITSGroups I II III VI 5-Year Metastasis 89% 58% 38% 14% free Survival10-Year Metastasis 72% 41% 17%  4% free Survival TNM Stage I II III5-Year Metastasis 83% 80% 47% free Survival 10-Year Metastasis 67% 58%30% free Survival

Example 4 IMP3, an Oncofetal Protein, Promotes Tumor Invasion andPredicts Progression of Cervical Intraepithelial Neoplasia into InvasiveCancer Introduction

Despite decades of effort, cervical cancer remains the second leadingcause of cancer related death in women at 288,000 per year worldwide⁽¹⁾.Cervical squamous intraepithelial lesion (SIL)⁽²⁾ or cervicalintraepithelial neoplasia (CIN)⁽³⁾ is a precancerous condition, and itstreatment can prevent the development of invasive cervicalcarcinomas⁽²⁾. It is evident that morphologically defined squamousintraepithelial lesions represent a heterogeneous group and thatprogression of high grade squamous intraepithelial lesions (HGSIL) intoinvasive squamous cell carcinoma is unpredictable. Currently, it isestimated that about 10-30% of HGSIL will develop into invasivecarcinomas if left untreated^((4,5,6)). Standard treatments for allpatients with HGSIL are local excisional surgical procedures, such asthe loop electrical excision procedure (LEEP) or cold knife coneexcision⁽⁷⁾. These procedures can damage the cervical stroma in waysthat lead to cervical stenosis or incompetence^((8,9,10)). This cancause significant morbidity for women of child-bearing age, increasingthe risk of preterm delivery, low birth-weight infants and prematurerupture of membranes^((8,9,10)). Currently, approximately 750,000 womenare diagnosed with squamous intraepithelial lesions each year in theUnited States, and the majority of these patients undergo surgicaltreatment^((11,12)). If the majority (approximately 70-80%) of highgrade squamous intraepithelial lesions that will not develop intoinvasive cancer could be identified, then these patients could be sparedthe current surgical procedure. This would benefit the outcome of anyfuture pregnancies in this group of women^((8,9,10)) and also reducehealth care costs. Therefore, it is very important to establish methodsto identify squamous intraepithelial lesions that have the potential toprogress to invasive cancer. Although many efforts have been made,especially in developing biomarkers, to selectively identify high riskpatients^((13,14)) there has been limited success^((15,16)).

Methods Patients and Tumor Samples

We obtained formalin-fixed, paraffin-embedded tissue samples from 1249patients with cervical biopsies (n=947), and LEEP/hysterectomy (n=302),from the archives at the University of Massachusetts Medical Center,Worcester, Mass., USA. Among 1249 patients, 79 patients were diagnosedinvasive squamous cell carcinoma, 895 patients were HGSIL, 108 patientswere low grade SIL (LGSIL), and 167 patients were negative for dysplasia(Table 1). To study the expression of IMP3 in all cervical lesions, wefirst obtained 586 cases of cervical lesions (no dysplasia, N=167;LGSIL, N=108; HGSIL, N=223 and invasive squamous cell carcinoma, N=79)between January 1997, and July 2007. To study IMP3 positivity insquamous intraepithelial lesions for the detection of a high risk groupof patients with HGSILs who will develop invasive carcinomas, we studiedall patients with cervical biopsies diagnosed as HGSIL and withsubsequent LEEP or hysterectomy (N=710) between January 1997 andDecember 2006 for our clinical follow-up study.

Immunohistochemical Analysis

Immunohistochemical studies were performed on 51 μm sections offormalin-fixed, paraffin-embedded tissue from cervical biopsy,excisional biopsy and hysterectomy specimens. Antigen retrieval wascarried out with 0.01 mol/L citrate buffer at pH 6.0, in an 800-Wmicrowave oven for 15 minutes before immunostaining. The slides werestained on the DAKO Autostainer (DAKO Corporation, Carpinteria, Calif.)using the EnVision (DAKO) staining reagents. The sections were firstblocked for endogenous protein binding and peroxidase activity with anapplication of Dual Endogenous Block (DAKO) for 10 minutes, followed bya buffer wash. The sections were then incubated with a mouse monoclonalantibody specific for IMP3 (L523S, DAKO) at a 2.0 μg/ml concentrationfor 30 minutes. Sections were then incubated with the EnVision+Dual Linkreagent (a polymer conjugated with goat-anti-mouse-Ig, and horseradishperoxidase) for 30 minutes, and treated with diaminobenzidine (DAB) andhydrogen peroxide, to produce the visible brown pigment. The sectionswere counterstained with hematoxylin, dehydrated, and coverslipped withpermanent media. Sections of urothelial carcinoma with known positivityof IMP3 were used as positive controls for IMP3 staining. Negativecontrols were performed by replacing the primary antibody with nonimmuneIgG.

Morphological Evaluation

The diagnosis of low and high grade CIN, and SCC was established byexamination of hematoxylin and eosin stained sections by twopathologists (DL and ZJ). Positive staining of IMP3 was defined as adark brown cytoplasmic staining pattern in the tumor epithelial cells,which was easily observed at low power magnification (<40×). Scant finegranular background staining of epithelial cells, which cannot be seenat low power magnification (≦40×), or no staining at all was considerednegative.Cell Culture and Small Interference RNA (siRNA) TransfectionThe cervical cancer cell line (HeLa cell) was maintained in DMEM withhigh glucose (GIBCO, Carlsbad, Calif.), containing 10% FBS andantibiotics at 37° C. incubator with 5% CO₂. For siRNA transfection,2×10⁵ cells were passed into antibiotic-free DMEM media in a 6-wellplate. On the next day, 20 or 40 nM of non-target siRNA or SMARTpoolsiRNA of human IMP3 (Dharmacon, Lafayette, Colo.) were transfected intoHeLa cells with Lipofectamine 2000 (Invitrogen, Carlsbad, Calif.),according to the manufacture protocol. All transfected cells were grownin a 37° C. incubator with 5% CO₂ for up to 72 hours for futureexperiments. To assess transfection efficiency, Block-It™ Fluorescentoligo (Invitrogen) was transfected under the same condition for controlor IMP3 siRNA. Transfected cells were photographed under phase-contrastmicroscope.

RT-PCR

To assess IMP3 knockdown efficiency by RT-PCR, siRNA transfected HeLacells were trypsinized and collected for total RNA extraction usingRNeasy Mini kit (QIAGEN, Valencia, Calif.). Two micrograms of total RNAwas used for reverse transcription using SuperScript III (Invitrogen).For RT-PCR, 2 μl of reverse-transcribed first-strand cDNA were used ineach PCR reaction with HotStar Taq Plus Master Mix (QIAGEN). RT-PCRprimers for IMP3 were: forward 5′-AGTGGGAGGTGCTGGATAGTT (SEQ ID No. 9)and reverse 5′-CTGGGTCTGTTTGGTGATGTT (SEQ ID No. 10). PCR program was asfollows: 95° C. for 5 minutes, followed by 95° C. for 30 seconds, 58° C.for 30 seconds, 72° C. for 30 seconds with a total of 26 cycles. PCRproducts were resolved into 1.2% agarose gel and photographed under UVillumination. GAPDH served as the loading control.

Western Blot Analysis

To assess the level of IMP3 protein expression after knockdown, Westernblotting was performed according to our previous method⁽²⁶⁾. Briefly, analiquot of HeLa cells transfected with control siRNA or siIMP3 for 72hours was re-suspended into RIPA butter (Boston BioProduct, Boston,Mass.) with complete protease inhibitors (Roche Diagnostics, Mannheim,Germany) for whole cell extract. A total of 30 μg of proteins wasresolved into 10% SDS-PAGE gel for IMP3 Western blotting, using a mousemonoclonal primary antibody against human IMP3 (DAKO) and anti-Actin(Santa Cruz Biotechnology, Santa Cruz, Calif.) served as the loadingcontrol.

Cell Proliferation Assay

To examine cell proliferation after IMP3 knockdown, cell proliferationreagent WST-1 (Roche Diagnostics) was used according to the manufactor'sinstructions. Briefly, 5×10³ HeLa cells were seeded into each well of a96-well plate in a final volume of 100 μl/well, and cells were culturedin a 37° C. incubator with 5% CO₂. On the next day, cells weretransfected with Control or siIMP3 using Lipofectamine 2000. At 24, 48,and 72 hours of siRNA transfection, 10 μl of WST-1 were added directlyinto each well and cells were incubated in a 37° C. incubator with 5%CO₂ for 1 hour. The absorbance of each well was measured with a BeckmanCoulter DTX 880 Multimode Detector (Beckman, Miami, Fla.) at awavelength of 450 nm and reference wavelength of 620 nm. An averageabsorbance (0D450-0D620) was calculated based on ten independentsamples.

Cell Migration Assay

HeLa cell migratory ability was assessed by the Transwell assay asdescribed previously with minor modification⁽³³⁾. Briefly, Transwell(Corning Incorporated, Corning, N.Y.) was coated with 15 μg/ml Laminin(BD Biosciences, San Jose, Calif.) at 4° C. overnight and then blockedby plain DMEM media for 1 hour at 37° C. incubator. HeLa cellstransfected with either Control or siIMP3 for 72 hours were trypsinizedand re-suspended into DMEM with 2.5% filtered BSA to a concentration of4×10⁵ cells/ml. One hundred microliter of the cells were seeded intoeach Transwell that was incubated in a 24-well plate containing 600μl/well of NIH3T3 conditioned media. Cells were cultured in a 37° C.incubator with 5% CO₂ for 4 hours. Cells inside the Transwell wereswabbed by a Q-tip followed by fixation in methanol for 10 minutes atroom temperature. Each Transwell was rinsed 5 times in distilled waterand the inside was swabbed again by a Q-tip. After air-drying, eachTranswell was put onto 20 μl of mounting medium containing DAPI (VectorLaboratories, Burlingame, Calif.) on a cover slip. Migratory cellsoutside the bottom of the Transwell were visualized under a fluorescentmicroscope at 20× magnification. For quantification, five representativefields were photographed and total number of cells was counted. Resultswere reported as an average of six independent samples.

Statistical Analysis

Invasive cancer-free survival rates by IMP3 status of all patients(N=710) with HGSIL in their cervical biopsies undergoing LEEP orhysterectomy were estimated by the Kaplan-Meier method and evaluatedusing log-rank test for univariate analysis. Invasive cancer-freesurvival was measured from the date of cervical biopsy to the date ofdiagnosis of invasive carcinoma by LEEP or hysterectomy. As the standardtreatment in the United States for all patients with HGSIL is localexcisional surgical procedures (e.g. LEEP) or hysterectomy after adiagnosis of HGSIL⁽⁴⁾. Most of our patients with HGSILs were treated bya resection procedure soon after their diagnoses. The median follow-uptime was 44 days (range=2 to 880 days). The median follow-up time forthe IMP3 negative group (N=551) was 46 days (range=2 to 880 days) andfor the IMP3 positive group (N=159) was 41 days (range=4 to 810 days).The distribution of every baseline variable was compared between IMP3positive and IMP3 negative subgroups using a Student's t-test forcontinuous variables and Fisher's exact test for categorical variables.A two-sided P-value of less than 0.05 was considered to indicate thestatistical significance.

Results

IMP3 expression is significantly elevated in invasive cancer and a smallgroup of HGSILs.

TABLE 9 Clinicopathological Characteristics of Cervical SquamousIntraepithelial Lesion (SIL) and Invasive Cancer Patients (N = 1249)Characteristic IMP3+ (n = 216) IMP3− (n = 1033) p-value Age (years)34.93 ± 11.86 34.85 ± 11.61 0.928* Diagnosis <0.0001** No Dysplasia 0(0%) 167 (100%) Low Grade SIL 0 (0%) 108 (100%) High Grade SIL 140(16%)  755 (84%)  Invasive Cancer 76 (96%) 3 (4%) *Student's t-test;**Fisher's exact test.

Table 9 provides the relevant clinical characteristics of 1249 patientswith cervical lesions. Age was not associated with IMP3 status(P=0.928). IMP3 expression was strongly associated with HGSIL andinvasive squamous carcinoma. The expression of IMP3 was found in thecytoplasm of HGSIL cells and invasive tumor cells. IMP3 expression wasnot identified in patients with LGSIL (N=108) or negative for dysplasia(N=167, Table 9). In contrast, 76 (96%) of 79 invasive cancers showedIMP3 expression (Table 9). 140 of the 895 (16%) patients with HGSIL werepositive for IMP3 (Table 9).

Prognostic Value of IMP3 in HGSIL for Invasive Cancer

710 patients who had HGSIL without invasive cancer in their cervicalbiopsies and had follow-up LEEP or hysterectomy were included in ourfollow-up study. A small portion [38 of 710 (5%)] of patients were foundto have invasive cancer in their follow-up LEEP or hysterectomy. IMP3expression was found in 159 of 710 (22%) HGSILs and 551 of 710 HGSILs(78%) were negative for IMP3. Kaplan-Meier invasive cancer-free survivalcurves showed that no patients (N=551) with IMP3-negative HGSILs hadinvasive cancer whereas 38 of 159 (24%) patients with IMP3-positiveHGSILs in their cervical biopsies were shown to have invasive cancer intheir follow-up LEEP or hysterectomy (P<0.0001).

IMP3 Promotes the Migration of Cervical Cancer Cells

We next analyzed the potential role of IMP3 in promoting the migrationof cervical cancer cells in vitro. To test the hypothesis that IMP3 mayplay a role in cancer cell migration, we used the human cervical cancer(HeLa) cell line as a model. These cells, which express IMP3, weretransfected with either 20 or 40 nM of SMARTpool small interfering RNAfor IMP3 (siIMP3) or a non-targeting pool of siRNA (Control) for 72hours. The siRNA transfection efficiency was confirmed by transfectionof Block-It™ FITC labeled siRNA, in which approximately 90% of cellsgained green fluorescence (data not shown). We observed that IMP3 mRNAand protein expression was reduced significantly by siIMP3 in comparisonto the control siRNA. To determine whether IMP3 silencing affected themigration of HeLa cells, a Transwell migration assay was performed 72hours after transfection of siIMP3 or control siRNA. Transfection ofsiIMP3 caused a marked reduction in HeLa cell migration in comparison tocontrol siRNA (FIG. 3C). A two-tail Student T-test showed that thisdifference is significant (p=2.5×10⁻⁸). However, the reduction of IMP3did not alter the growth rate of HeLa cells as indicated by WST-1 cellproliferation assay.

Discussion

In this study, we demonstrate that the expression of IMP3 in cervicalcancer cells is highly associated with invasive capability and IMP3expression in the high-grade intraepithelial lesions is predictive oftumor invasion. Therefore, IMP3 is able to serve as a biomarker whichwill provide important prognostic information for patients withpre-invasive cervical lesions.

There are several attractive features for the use of IMP3 expression asa biomarker in cervical lesions. First, the expression of IMP3 wassignificantly increased not only in invasive squamous cell carcinoma butmost importantly also in a subgroup of patients with high gradedysplasia who have invasive cancer in their follow-up excisionalbiopsies. We found that 24% of patients with IMP3 positivity in theirHGSILs have invasive cancer in their follow-up tissue resections.Therefore, the expression of IMP3 in cervical biopsies can identify asubgroup of patients who are at risk of progressing into invasivecarcinomas.

Second, we have demonstrated that the sub group of IMP3-negative HGSILsis not associated with invasive carcinoma. All 551 patients withIMP3-negative HGSILs were invasive cancer free in their follow-up tissueresections. Therefore, IMP3-negative HGSIL has a 100% negativepredictive value for invasive cancer. As far as we know, there have notbeen any other biomarkers reported for cervical lesions that have such apowerful negative predictive value. If these findings are validated inadditional clinical trials then it might be possible to change thefollow-up procedures from LEEP to follow-up biopsy and observation forthose patients with IMP3-negative HGSILs in their biopsies. The obviousimportance of identifying patients at low risk of cancer progression isthat it would both spare them the morbidity of the surgical procedures,and also save the health care system money.

Third, IMP3 immunohistochemical staining is a simple, inexpensive andreliable test. As most patients with high-grade dysplasias undergobiopsy, cervical biopsy tissue is routinely available forimmunohistochemical staining so that this assay could be easily appliedin routine clinical practice for all patients with cervical biopsies.Fourth, our in vitro assays strongly support our clinical data that IMP3may play an important role in cancer cell invasion. A previous studyshowed that IMP family members can control cancer cell invasion in vitro(32). We confirm and extend this analysis to show that reduction of IMP3expression alone in cervical cancer cells is able to significantlydecrease cancer cell migration. Our findings should enhance theunderstanding on cervical cancer oncogenesis as well. The establishedthree pathogenetic steps in cervical carcinogenesis include infection ofhigh-risk type HPV, initiation of clonal expansion of neoplastic cellswith deregulated expression of viral oncogenes, and finally progressioninto tumor invasion^((4,6)). Molecular markers associated with step 1and 2 may have been identified^((13,14,15,16)). IMP3 could be a crucialfactor that is involved in the migration event from the intraepithelialneoplastic cells into the invasive cancer. Exactly how IMP3 mightregulate these processes is not defined by our studies but it has beensuggested that IMP proteins regulate the expression of moleculesinvolved in adhesion and invasion, presumably through RNA binding⁽³²⁾.There is currently no evidence of association between HPV infection andIMP3 expression.

In summary, our study suggests that IMP3 is the first specific molecularmarker that identifies the invasive potential of cervical squamousintraepithelial lesions. This finding is significant as it may impactcurrent clinical practice. It provides a real possibility of an entirelynew molecular approach in examining cervical cancer precursors ratherthan our current morphological classification. Such a new approach couldimprove cervical cancer prevention by reducing the prevalence ofnon-necessary surgeries and provide a simple, cost-efficient molecularand biological testing method, which may reduce cervical cancer relatedhealthcare costs that are currently at estimated at 6 billion dollarseach year in the United States alone and more than the combined costs ofall other female related cancers⁽³⁴⁾

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EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents of the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1. A method for determining the prognosis of a subject having a cervicalcarcinoma, comprising the steps of: (a) obtaining from the subject aprimary tumor biopsy of the cervix; and (b) determining the presence orlevel of IMP3 in the primary tumor, wherein the presence of IMP3 in theprimary tumor of the subject indicates that the prognosis of the subjectis poor and an essentially undetectable level of IMP3 in the primarytumor of the subject indicates that the prognosis of the subject isgood.
 2. The method of claim 1, wherein the subject has a cervicalsquamous intraepithelial lesion (SIL) or cervical intraepithelialneoplasia (CIN).
 3. The method of claim 1, further comprisingdetermining at least one other factor, the presence, absence or level ofwhich reasonably correlates with the prediction of invasion from highgrade squamous intraepithelial lesion.
 4. The method of claim 3, furthercomprising determining the stage of the primary tumor.
 5. The method ofclaim 1, wherein the level of IMP3 is compared to a control value,wherein the control value is the level of IMP3 in non-cancerous cells ofthe same origin as those of the primary tumor or the level of IMP3 incells of a primary tumor of the same type as that in the subject from asubject having a good prognosis.
 6. The method of claim 1, whereindetermining the presence or level of IMP3 comprises determining thepresence or level of IMP3 protein.
 7. The method of claim 6, whereindetermining the presence or level of IMP3 protein comprisesimmunohistochemical staining.
 8. The method of claim 7, comprising usinga computerized image analyzer for quantitative analysis.
 9. The methodof claim 1, wherein the primary tumor is removed from the subject.
 10. Akit comprising an agent for detecting the presence or level of IMP3 anda control IMP3 value.
 11. The kit of claim 10, wherein the agent fordetecting the presence or level of IMP3 is an antibody or a fragmentthereof.
 12. The kit of claim 10, further comprising at least one otheragent for detecting the presence or level of a biomarker other thanIMP3.
 13. A method for monitoring the progression of a cervicalcarcinoma in a subject, comprising detecting the presence or level ofIMP3 in a primary cervical tumor of the subject over time, wherein anincrease in the level of IMP3 in the primary tumor of the subject overtime indicates that the in situ cancer is becoming invasive cancer. 14.The method of claim 13, wherein the subject has a cervical squamousintraepithelial lesion (SIL) or cervical intraepithelial neoplasia(CIN).
 15. The method of claim 13, wherein determining the presence orlevel of IMP3 comprises determining the presence or level of the IMP3protein.
 16. The method of claim 13, wherein determining the presence orlevel of IMP3 comprises determining the presence or level of IMP3 RNA.17. A method for treating a subject having a cervical carcinoma,comprising (i) determining whether the level of IMP3 in a cervical tumorobtained from the subject is abnormally high; and if the level is high,excising the tumor and if the level is low or undetectable, not excisingthe tumor.
 18. The method of claim 17, wherein the excision is performedusing the loop electrical excision procedure (LEEP).
 19. The method ofclaim 17, wherein the excision is performed using the cold knife coneexcision procedure.